skunkworks: old.xml annotate

annotate old.xml @ 34:c6fdf2c6d0f4 draft

Citations added (thanks John!) and a few more output formats for Alistair Chilcott

author	fubar
date	Thu, 28 Aug 2014 02:33:05 -0400
parents
children

rev	line source
34 c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	1 <tool id="rgedgeRpaired" name="edgeR" version="0.20">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	2 <description>1 or 2 level models for count data</description>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	3 <requirements>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	4 <requirement type="package" version="2.12">biocbasics</requirement>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	5 <requirement type="package" version="3.0.1">package_r3</requirement>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	6 </requirements>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	7
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	8 <command interpreter="python">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	9 rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "edgeR"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	10 --output_dir "$html_file.files_path" --output_html "$html_file" --output_tab "$outtab" --make_HTML "yes"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	11 </command>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	12 <inputs>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	13 <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	14 help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	15 <param name="title" type="text" value="edgeR" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	16 <sanitizer invalid_char="">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	17 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	18 </sanitizer>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	19 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	20 <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	21 <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	22 multiple="true" use_header_names="true" size="120" display="checkboxes">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	23 <validator type="no_options" message="Please select at least one column."/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	24 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	25 <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	26 <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	27 multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	28 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	29 <param name="subjectids" type="text" optional="true" size="120" value = ""
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	30 label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in input"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	31 help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter '1,2,1,2'">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	32 <sanitizer>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	33 <valid initial="string.digits"><add value="," /> </valid>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	34 </sanitizer>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	35 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	36 <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	37 help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	38 <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	39 label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	40 help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	41 <conditional name="DESeq">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	42 <param name="doDESeq" type="select"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	43 label="Run the same model with DESeq2 and compare findings"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	44 help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	45 <option value="F" selected="true">Do not run DESeq2</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	46 <option value="T">Run DESeq2 (only works if NO second GLM factor supplied at present)</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	47 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	48 <when value="T">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	49 <param name="DESeq_fitType" type="select">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	50 <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	51 <option value="local">Local fit - use this if parametric fails</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	52 <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	53 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	54 </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	55 <when value="F"> </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	56 </conditional>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	57 <param name="doVoom" type="boolean" truevalue="T" checked='false' falsevalue="F" size="1" label="Run the same model with VOOM transformation and limma."/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	58 <conditional name="camera">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	59 <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	60 help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	61 <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	62 <option value="T">Run GSEA tests with the Camera algorithm</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	63 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	64 <when value="T">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	65 <conditional name="gmtSource">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	66 <param name="refgmtSource" type="select"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	67 label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	68 <option value="indexed" selected="true">Use a built-in gene set</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	69 <option value="history">Use a gene set from my history</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	70 <option value="both">Add a gene set from my history to a built in gene set</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	71 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	72 <when value="indexed">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	73 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	74 <options from_data_table="gseaGMT_3.1">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	75 <filter type="sort_by" column="2" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	76 <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	77 </options>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	78 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	79 </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	80 <when value="history">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	81 <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	82 </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	83 <when value="both">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	84 <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	85 <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	86 <options from_data_table="gseaGMT_3.1">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	87 <filter type="sort_by" column="2" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	88 <validator type="no_options" message="No GMT v3.1 files are available - please fix tool_data_table and loc files"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	89 </options>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	90 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	91 </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	92 </conditional>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	93 </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	94 <when value="F">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	95 </when>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	96 </conditional>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	97 <param name="priordf" type="integer" value="20" size="3" label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n and prior.df = prior.n * residual.df"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	98 help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	99 <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	100 help="Conventional default value of 0.05 recommended"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	101 <param name="fdrtype" type="select" label="FDR (Type II error) control method"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	102 help="Use fdr or bh typically to control for the number of tests in a reliable way">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	103 <option value="fdr" selected="true">fdr</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	104 <option value="BH">Benjamini Hochberg</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	105 <option value="BY">Benjamini Yukateli</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	106 <option value="bonferroni">Bonferroni</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	107 <option value="hochberg">Hochberg</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	108 <option value="holm">Holm</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	109 <option value="hommel">Hommel</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	110 <option value="none">no control for multiple tests</option>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	111 </param>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	112 </inputs>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	113 <outputs>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	114 <data format="tabular" name="outtab" label="${title}.xls"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	115 <data format="html" name="html_file" label="${title}.html"/>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	116 </outputs>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	117 <stdio>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	118 <exit_code range="4" level="fatal" description="Number of subject ids must match total number of samples in the input matrix" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	119 </stdio>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	120 <tests>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	121 <test>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	122 <param name='input1' value='test_bams2mx.xls' ftype='tabular' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	123 <param name='treatment_name' value='case' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	124 <param name='title' value='edgeRtest' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	125 <param name='useNDF' value='' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	126 <param name='fdrtype' value='fdr' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	127 <param name='priordf' value="0" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	128 <param name='fdrthresh' value="0.05" />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	129 <param name='control_name' value='control' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	130 <param name='subjectids' value='' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	131 <param name='Treat_cols' value='3,4,5,9' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	132 <param name='Control_cols' value='2,6,7,8' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	133 <output name='outtab' file='edgeRtest1out.xls' compare='diff' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	134 <output name='html_file' file='edgeRtest1out.html' compare='diff' lines_diff='20' />
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	135 </test>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	136 </tests>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	137
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	138 <configfiles>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	139 <configfile name="runme">
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	140 <![CDATA[
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	141 ##
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	142 ## edgeR.Rscript
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	143 ## updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	144 ## Performs DGE on a count table containing n replicates of two conditions
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	145 ##
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	146 ### Original edgeR code by: S.Lunke and A.Kaspi
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	147 reallybig = log10(.Machine\$double.xmax)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	148 reallysmall = log10(.Machine\$double.xmin)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	149 library('stringr')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	150 library('gplots')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	151 library('edgeR')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	152
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	153 hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	154 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	155 ### Perform clustering for significant pvalues after controlling FWER
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	156 samples = colnames(cmat)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	157 gu = unique(group)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	158 if (length(gu) == 2) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	159 col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	160 pcols = unlist(lapply(group,col.map))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	161 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	162 colours = rainbow(length(gu),start=0,end=4/6)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	163 pcols = colours[match(group,gu)]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	164 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	165 gn = rownames(cmat)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	166 dm = cmat[(! is.na(gn)),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	167 ### remove unlabelled hm rows
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	168 nprobes = nrow(dm)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	169 if (nprobes > nsamp) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	170 dm =dm[1:nsamp,]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	171 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	172 newcolnames = substr(colnames(dm),1,20)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	173 colnames(dm) = newcolnames
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	174 pdf(outpdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	175 heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	176 Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	177 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	178 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	179
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	180 hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	181 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	182 ## for 2 groups only was
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	183 ## col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	184 ## pcols = unlist(lapply(group,col.map))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	185 gu = unique(group)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	186 colours = rainbow(length(gu),start=0.3,end=0.6)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	187 pcols = colours[match(group,gu)]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	188 nrows = nrow(cmat)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	189 mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	190 if (nrows > nsamp) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	191 cmat = cmat[c(1:nsamp),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	192 mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	193 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	194 newcolnames = substr(colnames(cmat),1,20)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	195 colnames(cmat) = newcolnames
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	196 pdf(outpdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	197 heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	198 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	199 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	200
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	201 qqPlot = function(descr='Title',pvector, ...)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	202 ## stolen from https://gist.github.com/703512
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	203 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	204 o = -log10(sort(pvector,decreasing=F))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	205 e = -log10( 1:length(o)/length(o) )
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	206 o[o==-Inf] = reallysmall
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	207 o[o==Inf] = reallybig
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	208 pdfname = paste(gsub(" ","", descr , fixed=TRUE),'pval_qq.pdf',sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	209 maint = paste(descr,'QQ Plot')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	210 pdf(pdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	211 plot(e,o,pch=19,cex=1, main=maint, ...,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	212 xlab=expression(Expected~~-log[10](italic(p))),
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	213 ylab=expression(Observed~~-log[10](italic(p))),
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	214 xlim=c(0,max(e)), ylim=c(0,max(o)))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	215 lines(e,e,col="red")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	216 grid(col = "lightgray", lty = "dotted")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	217 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	218 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	219
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	220 smearPlot = function(DGEList,deTags, outSmear, outMain)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	221 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	222 pdf(outSmear)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	223 plotSmear(DGEList,de.tags=deTags,main=outMain)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	224 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	225 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	226 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	227
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	228 boxPlot = function(rawrs,cleanrs,maint,myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	229 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	230 nc = ncol(rawrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	231 for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	232 fullnames = colnames(rawrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	233 newcolnames = substr(colnames(rawrs),1,20)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	234 colnames(rawrs) = newcolnames
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	235 newcolnames = substr(colnames(cleanrs),1,20)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	236 colnames(cleanrs) = newcolnames
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	237 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"sampleBoxplot.pdf",sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	238 defpar = par(no.readonly=T)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	239 pdf(pdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	240 l = layout(matrix(c(1,2),1,2,byrow=T))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	241 print.noquote('raw contig counts by sample:')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	242 print.noquote(summary(rawrs))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	243 print.noquote('normalised contig counts by sample:')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	244 print.noquote(summary(cleanrs))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	245 boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	246 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	247 boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	248 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	249 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	250 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"samplehistplot.pdf",sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	251 nc = ncol(rawrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	252 print.noquote(paste('Using ncol rawrs=',nc))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	253 ncroot = round(sqrt(nc))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	254 if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	255 m = c()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	256 for (i in c(1:nc)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	257 rhist = hist(rawrs[,i],breaks=100,plot=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	258 m = append(m,max(rhist\$counts))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	259 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	260 ymax = max(m)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	261 pdf(pdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	262 par(mfrow=c(ncroot,ncroot))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	263 for (i in c(1:nc)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	264 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	265 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	266 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	267 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	268 par(defpar)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	269
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	270 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	271
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	272 cumPlot = function(rawrs,cleanrs,maint,myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	273 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	274 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	275 defpar = par(no.readonly=T)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	276 pdf(pdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	277 par(mfrow=c(2,1))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	278 lrs = log(rawrs,10)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	279 lim = max(lrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	280 hist(lrs,breaks=100,main=paste('Before:',maint),xlab="Reads (log)",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	281 ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	282 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	283 lrs = log(cleanrs,10)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	284 hist(lrs,breaks=100,main=paste('After:',maint),xlab="Reads (log)",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	285 ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	286 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	287 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	288 par(defpar)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	289 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	290
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	291 cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	292 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	293 pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	294 pdf(pdfname)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	295 par(mfrow=c(2,1))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	296 lastx = max(rawrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	297 rawe = knots(ecdf(rawrs))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	298 cleane = knots(ecdf(cleanrs))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	299 cy = 1:length(cleane)/length(cleane)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	300 ry = 1:length(rawe)/length(rawe)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	301 plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	302 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	303 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	304 plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	305 ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	306 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	307 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	308 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	309
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	310
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	311
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	312 doGSEA = function(y=NULL,design=NULL,histgmt="",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	313 bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	314 ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	315 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	316 genesets = c()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	317 if (bigmt > "")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	318 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	319 bigenesets = readLines(bigmt)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	320 genesets = bigenesets
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	321 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	322 if (histgmt > "")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	323 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	324 hgenesets = readLines(histgmt)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	325 if (bigmt > "") {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	326 genesets = rbind(genesets,hgenesets)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	327 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	328 genesets = hgenesets
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	329 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	330 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	331 print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	332 genesets = strsplit(genesets,'\t')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	333 ##### tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	334 outf = outfname
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	335 head=paste(myTitle,'edgeR GSEA')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	336 write(head,file=outfname,append=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	337 ntest=length(genesets)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	338 urownames = toupper(rownames(y))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	339 upcam = c()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	340 downcam = c()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	341 for (i in 1:ntest) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	342 gs = unlist(genesets[i])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	343 g = gs[1] #### geneset_id
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	344 u = gs[2]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	345 if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	346 glist = gs[3:length(gs)] #### member gene symbols
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	347 glist = toupper(glist)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	348 inglist = urownames %in% glist
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	349 nin = sum(inglist)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	350 if ((nin > minnin) && (nin < maxnin)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	351 ### print(paste('@@found',sum(inglist),'genes in glist'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	352 camres = camera(y=y,index=inglist,design=design)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	353 if (camres) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	354 rownames(camres) = g
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	355 ##### gene set name
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	356 camres = cbind(GeneSet=g,URL=u,camres)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	357 if (camres\$Direction == "Up")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	358 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	359 upcam = rbind(upcam,camres) } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	360 downcam = rbind(downcam,camres)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	361 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	362 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	363 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	364 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	365 uscam = upcam[order(upcam\$PValue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	366 unadjp = uscam\$PValue
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	367 uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	368 nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	369 dscam = downcam[order(downcam\$PValue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	370 unadjp = dscam\$PValue
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	371 dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	372 ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	373 write.table(uscam,file=paste('upCamera',outfname,sep='_'),quote=F,sep='\t',row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	374 write.table(dscam,file=paste('downCamera',outfname,sep='_'),quote=F,sep='\t',row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	375 print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	376 write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	377 print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	378 write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	379 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	380
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	381
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	382
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	383 edgeIt = function (Count_Matrix,group,outputfilename,fdrtype='fdr',priordf=5,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	384 fdrthresh=0.05,outputdir='.', myTitle='edgeR',libSize=c(),useNDF=F,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	385 filterquantile=0.2, subjects=c(),mydesign=NULL,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	386 doDESeq=T,doVoom=T,doCamera=T,org='hg19',
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	387 histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	388 doCook=F,DESeq_fittype="parameteric")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	389 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	390 if (length(unique(group))!=2){
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	391 print("Number of conditions identified in experiment does not equal 2")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	392 q()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	393 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	394 require(edgeR)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	395 options(width = 512)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	396 mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	397 allN = nrow(Count_Matrix)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	398 nscut = round(ncol(Count_Matrix)/2)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	399 colTotmillionreads = colSums(Count_Matrix)/1e6
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	400 rawrs = rowSums(Count_Matrix)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	401 nonzerod = Count_Matrix[(rawrs > 0),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	402 nzN = nrow(nonzerod)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	403 nzrs = rowSums(nonzerod)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	404 zN = allN - nzN
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	405 print('**** Quantiles for non-zero row counts:',quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	406 print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	407 if (useNDF == "T")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	408 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	409 gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	410 lo = colSums(Count_Matrix[!gt1rpin3,])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	411 workCM = Count_Matrix[gt1rpin3,]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	412 cleanrs = rowSums(workCM)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	413 cleanN = length(cleanrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	414 meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	415 print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	416 maint = paste('Filter >= 1/million reads in >=',nscut,'samples')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	417 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	418 useme = (nzrs > quantile(nzrs,filterquantile))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	419 workCM = nonzerod[useme,]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	420 lo = colSums(nonzerod[!useme,])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	421 cleanrs = rowSums(workCM)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	422 cleanN = length(cleanrs)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	423 meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	424 print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	425 maint = paste('Filter below',filterquantile,'quantile')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	426 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	427 cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	428 allgenes <- rownames(workCM)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	429 print(paste("*** Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	430 rsums = rowSums(workCM)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	431 TName=unique(group)[1]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	432 CName=unique(group)[2]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	433 DGEList = DGEList(counts=workCM, group = group)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	434 DGEList = calcNormFactors(DGEList)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	435
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	436 if (is.null(mydesign)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	437 if (length(subjects) == 0)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	438 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	439 mydesign = model.matrix(~group)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	440 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	441 else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	442 subjf = factor(subjects)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	443 mydesign = model.matrix(~subjf+group)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	444 ### we block on subject so make group last to simplify finding it
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	445 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	446 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	447 print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	448 print.noquote('Using design matrix:')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	449 print.noquote(mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	450 DGEList = estimateGLMCommonDisp(DGEList,mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	451 comdisp = DGEList\$common.dispersion
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	452 DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	453 if (priordf > 0) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	454 print.noquote(paste("prior.df =",priordf))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	455 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = priordf)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	456 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	457 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	458 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	459 lastcoef=ncol(mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	460 print.noquote(paste('*** lastcoef = ',lastcoef))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	461 estpriorn = getPriorN(DGEList)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	462 predLFC1 = predFC(DGEList,prior.count=1,design=mydesign,dispersion=DGEList\$tagwise.dispersion,offset=getOffset(DGEList))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	463 predLFC3 = predFC(DGEList,prior.count=3,design=mydesign,dispersion=DGEList\$tagwise.dispersion,offset=getOffset(DGEList))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	464 predLFC5 = predFC(DGEList,prior.count=5,design=mydesign,dispersion=DGEList\$tagwise.dispersion,offset=getOffset(DGEList))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	465 DGLM = glmFit(DGEList,design=mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	466 DE = glmLRT(DGLM)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	467 #### always last one - subject is first if needed
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	468 logCPMnorm = cpm(DGEList,log=T,normalized.lib.sizes=T)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	469 logCPMraw = cpm(DGEList,log=T,normalized.lib.sizes=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	470 uoutput = cbind(
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	471 Name=as.character(rownames(DGEList\$counts)),
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	472 DE\$table,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	473 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	474 Dispersion=DGEList\$tagwise.dispersion,totreads=rsums,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	475 predLFC1=predLFC1[,lastcoef],
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	476 predLFC3=predLFC3[,lastcoef],
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	477 predLFC5=predLFC5[,lastcoef],
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	478 logCPMnorm,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	479 DGEList\$counts
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	480 )
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	481 soutput = uoutput[order(DE\$table\$PValue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	482 heatlogcpmnorm = logCPMnorm[order(DE\$table\$PValue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	483 goodness = gof(DGLM, pcutoff=fdrthresh)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	484 noutl = (sum(goodness\$outlier) > 0)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	485 if (noutl > 0) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	486 print.noquote(paste('***',noutl,'GLM outliers found'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	487 print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	488 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	489 print('*** No GLM fit outlier genes found')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	490 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	491 z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	492 pdf(paste(mt,"GoodnessofFit.pdf",sep='_'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	493 qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	494 abline(0,1,lwd=3)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	495 points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	496 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	497 print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	498 uniqueg = unique(group)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	499 sample_colors = match(group,levels(group))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	500 pdf(paste(mt,"MDSplot.pdf",sep='_'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	501 sampleTypes = levels(factor(group))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	502 print.noquote(sampleTypes)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	503 plotMDS.DGEList(DGEList,main=paste("MDS Plot for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	504 legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	505 grid(col="blue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	506 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	507 colnames(logCPMnorm) = paste( colnames(logCPMnorm),'N',sep="_")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	508 print(paste('Raw sample CPM',paste(colSums(logCPMraw,na.rm=T),collapse=',')))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	509 try(boxPlot(rawrs=logCPMraw,cleanrs=logCPMnorm,maint='TMM Normalisation',myTitle=myTitle))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	510 nreads = soutput\$totreads
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	511 print('*** writing output',quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	512 write.table(soutput,outputfilename, quote=FALSE, sep="\t",row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	513 rn = row.names(workCM)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	514 print.noquote('@@ rn')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	515 print.noquote(head(rn))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	516 reg = "^chr([0-9]+):([0-9]+)-([0-9]+)"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	517 genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	518 ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	519 testreg = str_match(rn,reg)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	520 nreads = uoutput\$totreads
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	521 if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	522 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	523 print("@@ using ucsc substitution for urls")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	524 urls = paste0(ucsc,"&position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",rn,"</a>")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	525 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	526 print("@@ using genecards substitution for urls")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	527 urls = paste0(genecards,rn,"\'>",rn,"</a>")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	528 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	529 tt = uoutput
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	530 print.noquote("*** edgeR Top tags\n")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	531 tt = cbind(tt,ntotreads=nreads,URL=urls)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	532 tt = tt[order(DE\$table\$PValue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	533 print.noquote(tt[1:50,])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	534 ### Plot MAplot
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	535 deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	536 nsig = length(deTags)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	537 print(paste('***',nsig,'tags significant at adj p=',fdrthresh),quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	538 if (nsig > 0) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	539 print('*** deTags',quote=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	540 print(head(deTags))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	541 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	542 deColours = ifelse(deTags,'red','black')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	543 pdf(paste(mt,"BCV_vs_abundance.pdf",sep='_'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	544 plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	545 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	546 dg = DGEList[order(DE\$table\$PValue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	547 outpdfname=paste(mt,"heatmap.pdf",sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	548 hmap2(heatlogcpmnorm,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=myTitle)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	549 outSmear = paste(mt,"Smearplot.pdf",sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	550 outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	551 smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	552 qqPlot(descr=myTitle,pvector=DE\$table\$PValue)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	553 if (doDESeq == T)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	554 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	555 ### DESeq2
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	556 require('DESeq2')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	557 print.noquote(paste('****subjects=',subjects,'length=',length(subjects)))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	558 if (length(subjects) == 0)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	559 {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	560 pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	561 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ Rx))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	562 } else {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	563 pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	564 deSEQds = DESeqDataSetFromMatrix(countData = workCM, colData = pdata, design = formula(~ subjects + Rx))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	565 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	566 deSeqDatsizefac <- estimateSizeFactors(deSEQds)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	567 deSeqDatdisp <- estimateDispersions(deSeqDatsizefac,fitType=DESeq_fittype)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	568 resDESeq <- nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	569 rDESeq = as.data.frame(results(resDESeq))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	570 srDESeq = rDESeq[order(rDESeq\$pvalue),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	571 write.table(srDESeq,paste(mt,'DESeq2_TopTable.xls',sep='_'), quote=FALSE, sep="\t",row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	572 topresults.DESeq <- rDESeq[which(rDESeq\$padj < fdrthresh), ]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	573 DESeqcountsindex <- which(allgenes %in% rownames(topresults.DESeq))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	574 DESeqcounts <- rep(0, length(allgenes))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	575 DESeqcounts[DESeqcountsindex] <- 1
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	576 pdf(paste(mt,"DESeq2_dispersion_estimates.pdf",sep='_'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	577 plotDispEsts(resDESeq)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	578 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	579 if (doCook) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	580 pdf(paste(mt,"DESeq2_cooks_distance.pdf",sep='_'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	581 W <- mcols(resDESeq)\$WaldStatistic_condition_treated_vs_untreated
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	582 maxCooks <- mcols(resDESeq)\$maxCooks
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	583 idx <- !is.na(W)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	584 plot(rank(W[idx]), maxCooks[idx], xlab="rank of Wald statistic", ylab="maximum Cook's distance per gene",
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	585 ylim=c(0,5), cex=.4, col="maroon")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	586 m <- ncol(dds)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	587 p <- 3
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	588 abline(h=qf(.75, p, m - p),col="darkblue")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	589 grid(col="lightgray",lty="dotted")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	590 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	591 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	592 counts.dataframe = as.data.frame(c())
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	593 norm.factor = DGEList\$samples\$norm.factors
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	594 topresults.edgeR <- soutput[which(soutput\$adj.p.value < fdrthresh), ]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	595 edgeRcountsindex <- which(allgenes %in% rownames(topresults.edgeR))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	596 edgeRcounts <- rep(0, length(allgenes))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	597 edgeRcounts[edgeRcountsindex] <- 1
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	598 if (doVoom == T) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	599 pdf(paste(mt,"voomplot.pdf",sep='_'))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	600 dat.voomed <- voom(DGEList, mydesign, plot = TRUE, normalize.method="quantil", lib.size = NULL)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	601 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	602 fit <- lmFit(dat.voomed, mydesign)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	603 fit <- eBayes(fit)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	604 rvoom <- topTable(fit, coef = length(colnames(mydesign)), adj = "BH", n = Inf)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	605 write.table(rvoom,paste(mt,'VOOM_topTable.xls',sep='_'), quote=FALSE, sep="\t",row.names=F)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	606 topresults.voom <- rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	607 voomcountsindex <- which(allgenes %in% rownames(topresults.voom))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	608 voomcounts <- rep(0, length(allgenes))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	609 voomcounts[voomcountsindex] <- 1
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	610 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	611 if ((doDESeq==T) \|\| (doVoom==T)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	612 if ((doVoom==T) && (doDESeq==T)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	613 vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	614 counts.dataframe <- data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	615 VOOM_limma = voomcounts, row.names = allgenes)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	616 } else if (doDESeq==T) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	617 vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	618 counts.dataframe <- data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	619 } else if (doVoom==T) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	620 vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	621 counts.dataframe <- data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	622 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	623
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	624 if (nrow(counts.dataframe > 1)) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	625 counts.venn <- vennCounts(counts.dataframe)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	626 vennf = paste(mt,'venn.pdf',sep='_')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	627 pdf(vennf)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	628 vennDiagram(counts.venn,main=vennmain,col="maroon")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	629 dev.off()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	630 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	631 } ### doDESeq or doVoom
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	632 if (doDESeq==T) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	633 cat("*** DESeq top 50\n")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	634 print(srDESeq[1:50,])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	635 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	636 if (doVoom==T) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	637 cat("*** VOOM top 50\n")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	638 print(rvoom[1:50,])
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	639 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	640 if (doCamera) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	641 doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	642 outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	643 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	644 uoutput
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	645
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	646 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	647 #### Done
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	648
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	649 #### sink(stdout(),append=T,type="message")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	650
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	651 doDESeq = $DESeq.doDESeq
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	652 ### make these 'T' or 'F'
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	653 doVoom = $doVoom
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	654 doCamera = $camera.doCamera
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	655 Out_Dir = "$html_file.files_path"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	656 Input = "$input1"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	657 TreatmentName = "$treatment_name"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	658 TreatmentCols = "$Treat_cols"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	659 ControlName = "$control_name"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	660 ControlCols= "$Control_cols"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	661 outputfilename = "$outtab"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	662 org = "$input1.dbkey"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	663 if (org == "") { org = "hg19"}
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	664 fdrtype = "$fdrtype"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	665 priordf = $priordf
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	666 fdrthresh = $fdrthresh
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	667 useNDF = "$useNDF"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	668 fQ = $fQ
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	669 myTitle = "$title"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	670 sids = strsplit("$subjectids",',')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	671 subjects = unlist(sids)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	672 nsubj = length(subjects)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	673 builtin_gmt=""
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	674 history_gmt=""
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	675
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	676 builtin_gmt = ""
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	677 history_gmt = ""
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	678 DESeq_fittype=""
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	679 #if $DESeq.doDESeq == "T"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	680 DESeq_fittype = "$DESeq.DESeq_fitType"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	681 #end if
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	682 #if $camera.doCamera == 'T'
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	683 #if $camera.gmtSource.refgmtSource == "indexed" or $camera.gmtSource.refgmtSource == "both":
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	684 builtin_gmt = "${camera.gmtSource.builtinGMT.fields.path}"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	685 #end if
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	686 #if $camera.gmtSource.refgmtSource == "history" or $camera.gmtSource.refgmtSource == "both":
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	687 history_gmt = "${camera.gmtSource.ownGMT}"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	688 history_gmt_name = "${camera.gmtSource.ownGMT.name}"
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	689 #end if
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	690 #end if
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	691 if (nsubj > 0) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	692 if (doDESeq) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	693 print('WARNING - cannot yet use DESeq2 for 2 way anova - see the docs')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	694 doDESeq = F
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	695 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	696 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	697 TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	698 CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	699 cat('Got TCols=')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	700 cat(TCols)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	701 cat('; CCols=')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	702 cat(CCols)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	703 cat('\n')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	704 useCols = c(TCols,CCols)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	705 if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	706 Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	707 snames = colnames(Count_Matrix)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	708 nsamples = length(snames)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	709 if (nsubj > 0 & nsubj != nsamples) {
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	710 options("show.error.messages"=T)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	711 mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	712 'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	713 write(mess, stderr())
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	714 quit(save="no",status=4)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	715 }
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	716
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	717 Count_Matrix = Count_Matrix[,useCols] ### reorder columns
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	718 if (length(subjects) != 0) {subjects = subjects[useCols]}
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	719 rn = rownames(Count_Matrix)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	720 islib = rn %in% c('librarySize','NotInBedRegions')
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	721 LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	722 Count_Matrix = Count_Matrix[subset(rn,! islib),]
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	723 group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	724 group = factor(group, levels=c(ControlName,TreatmentName))
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	725 colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	726 results = edgeIt(Count_Matrix=Count_Matrix,group=group,outputfilename=outputfilename,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	727 fdrtype='BH',priordf=priordf,fdrthresh=fdrthresh,outputdir='.',
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	728 myTitle='edgeR',useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	729 doDESeq=doDESeq,doVoom=doVoom,doCamera=doCamera,org=org,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	730 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fittype=DESeq_fittype)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	731 sessionInfo()
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	732 ]]>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	733 </configfile>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	734 </configfiles>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	735 <help>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	736
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	737 What it does
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	738
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	739 Performs digital gene expression analysis between a treatment and control on a count matrix.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	740 Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	741
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	742 Input
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	743
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	744 A matrix consisting of non-negative integers. The matrix must have a unique header row identifiying the samples, and a unique set of row names
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	745 as the first column. Typically the row names are gene symbols or probe id's for downstream use in GSEA and other methods.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	746
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	747 If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	748 put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	749 A list of integers, one for each subject or an empty string if samples are all independent.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	750 If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	751 Integers for samples that are not in the analysis must be present in the string as filler even if not used.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	752
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	753 So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	754 eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	755 8,9,1,1,2,2
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	756 as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	757
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	758 Output
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	759
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	760 A summary html page with links to the R source code and all the outputs, nice grids of helpful plot thumbnails, and lots
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	761 of logging and the top 50 rows of the topTable.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	762
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	763 The main topTables of results are provided as separate excelish tabular files.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	764
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	765 They include adjusted p values and dispersions for each region, raw and cpm sample data counts and shrunken (predicted) log fold change estimates.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	766 These are provided for downstream analyses such as GSEA and are predictions of the logFC you might expect to see
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	767 in an independent replication of your original experiment. Higher number means more shrinkage. Shrinkage is more extreme for low coverage features
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	768 so downstream analyses are more robust against strong effect size estimates based on relatively little experimental information.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	769
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	770 Note on prior.N
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	771
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	772 http://seqanswers.com/forums/showthread.php?t=5591 says:
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	773
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	774 prior.n
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	775
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	776 The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	777 You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	778 in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	779 tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	780 common likelihood the weight of one observation.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	781
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	782 In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	783 or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	784 you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	785 (squeezing) of the tagwise dispersions. How many samples do you have in your experiment?
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	786 What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	787 If you have more samples, then the tagwise dispersion estimates will be more reliable,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	788 so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	789
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	790
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	791 From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	792
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	793 Dear Dorota,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	794
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	795 The important settings are prior.df and trend.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	796
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	797 prior.n and prior.df are related through prior.df = prior.n * residual.df,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	798 and your experiment has residual.df = 36 - 12 = 24. So the old setting of
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	799 prior.n=10 is equivalent for your data to prior.df = 240, a very large
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	800 value. Going the other way, the new setting of prior.df=10 is equivalent
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	801 to prior.n=10/24.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	802
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	803 To recover old results with the current software you would use
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	804
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	805 estimateTagwiseDisp(object, prior.df=240, trend="none")
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	806
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	807 To get the new default from old software you would use
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	808
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	809 estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	810
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	811 Actually the old trend method is equivalent to trend="loess" in the new
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	812 software. You should use plotBCV(object) to see whether a trend is
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	813 required.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	814
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	815 Note you could also use
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	816
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	817 prior.n = getPriorN(object, prior.df=10)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	818
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	819 to map between prior.df and prior.n.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	820
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	821 Old rant on variable name changes in bioconductor versions
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	822
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	823 BioC authors sometimes make small mostly cosmetic changes to variable names (eg: from p.value to PValue)
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	824 often to make them more internally consistent or self describing. Unfortunately, these improvements
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	825 break existing code in ways that can take a while to track down that relies on the library in ways that can take a while to track down,
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	826 increasing downstream tool maintenance effort uselessly.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	827
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	828 Please, don't do that. It hurts us.
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	829
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	830
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	831 </help>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	832
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	833 </tool>
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	834
c6fdf2c6d0f4 Citations added (thanks John!) and a few more output formats for Alistair Chilcott fubar parents: diff changeset	835

Mercurial > repos > fubar > toolfactory

annotate old.xml @ 34:c6fdf2c6d0f4 draft