cummerbund: test-data/fpkmSCV.txt annotate

annotate test-data/fpkmSCV.txt @ 4:ba8fde59843d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

author	devteam
date	Tue, 21 Jul 2015 14:18:39 -0400
parents	587c425b4e76
children	78fcfc04fcfe

rev	line source
0 587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	1
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	3 Copyright (C) 2014 The R Foundation for Statistical Computing
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	4 Platform: x86_64-unknown-linux-gnu (64-bit)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	5
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	6 R is free software and comes with ABSOLUTELY NO WARRANTY.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	7 You are welcome to redistribute it under certain conditions.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	8 Type 'license()' or 'licence()' for distribution details.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	9
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	10 Natural language support but running in an English locale
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	11
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	12 R is a collaborative project with many contributors.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	13 Type 'contributors()' for more information and
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	14 'citation()' on how to cite R or R packages in publications.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	15
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	16 Type 'demo()' for some demos, 'help()' for on-line help, or
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	17 'help.start()' for an HTML browser interface to help.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	18 Type 'q()' to quit R.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	19
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	20 > ## Feature Selection ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	21 > get_features <- function(myGenes, f="gene") {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	22 + if (f == "isoforms")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	23 + return(isoforms(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	24 + else if (f == "tss")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	25 + return(TSS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	26 + else if (f == "cds")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	27 + return(CDS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	28 + else
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	29 + return(myGenes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	30 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	31 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	32 > ## Main Function ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	33 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	34 > library(argparse)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	35 Loading required package: proto
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	36 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	37 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	38 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	39 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	40 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	41 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	42 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	43 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	44 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	45 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	46 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	47 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	48 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	49 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	50 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	51 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	52 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	53 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	54 > parser$add_argument('--features', dest='features', action="store", default="genes")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	55 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	56 > parser$add_argument('--iter_max', dest='iter_max', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	57 > parser$add_argument('--genes', dest='genes', action="append")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	58 > parser$add_argument('--k', dest='k', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	59 > parser$add_argument('--x', dest='x', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	60 > parser$add_argument('--y', dest='y', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	61 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	62 > args <- parser$parse_args()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	63 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	64 > print(args)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	65 $border
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	66 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	67
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	68 $clustering
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	69 [1] "both"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	70
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	71 $count
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	72 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	73
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	74 $error_bars
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	75 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	76
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	77 $features
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	78 [1] "genes"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	79
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	80 $filename
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	81 [1] "plot-fpkmSCV-0.png"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	82
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	83 $gene_selector
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	84 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	85
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	86 $genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	87 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	88
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	89 $height
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	90 [1] 960
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	91
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	92 $input_database
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	93 [1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_49.dat"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	94
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	95 $iter_max
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	96 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	97
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	98 $k
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	99 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	100
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	101 $labcol
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	102 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	103
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	104 $labrow
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	105 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	106
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	107 $log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	108 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	109
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	110 $plotType
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	111 [1] "fpkmSCV"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	112
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	113 $replicates
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	114 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	115
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	116 $smooth
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	117 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	118
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	119 $summary
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	120 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	121
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	122 $width
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	123 [1] 1280
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	124
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	125 $x
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	126 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	127
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	128 $y
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	129 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	130
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	131 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	132 > #q()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	133 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	134 > ## Load cummeRbund library
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	135 > library("cummeRbund")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	136 Loading required package: BiocGenerics
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	137 Loading required package: parallel
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	138
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	139 Attaching package: ‘BiocGenerics’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	140
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	141 The following objects are masked from ‘package:parallel’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	142
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	144 clusterExport, clusterMap, parApply, parCapply, parLapply,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	145 parLapplyLB, parRapply, parSapply, parSapplyLB
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	146
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	147 The following object is masked from ‘package:stats’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	148
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	149 xtabs
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	150
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	151 The following objects are masked from ‘package:base’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	152
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	157 rownames, sapply, setdiff, sort, table, tapply, union, unique,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	158 unlist, unsplit
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	159
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	160 Loading required package: RSQLite
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	161 Loading required package: DBI
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	162 Loading required package: ggplot2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	163 Loading required package: reshape2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	164 Loading required package: fastcluster
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	165
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	166 Attaching package: ‘fastcluster’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	167
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	168 The following object is masked from ‘package:stats’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	169
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	170 hclust
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	171
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	172 Loading required package: rtracklayer
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	173 Loading required package: GenomicRanges
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	174 Loading required package: S4Vectors
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	175 Loading required package: stats4
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	176 Loading required package: IRanges
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	177 Loading required package: GenomeInfoDb
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	178 Loading required package: Gviz
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	179 Loading required package: grid
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	180
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	181 Attaching package: ‘cummeRbund’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	182
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	183 The following object is masked from ‘package:GenomicRanges’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	184
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	185 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	186
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	187 The following object is masked from ‘package:IRanges’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	188
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	189 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	190
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	191 The following object is masked from ‘package:BiocGenerics’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	192
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	193 conditions
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	194
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	195 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	196 > ## Initialize cuff object
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	197 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	198 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	199 > ## Print out info
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	200 > print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	201 CuffSet instance with:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	202 2 samples
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	203 87 genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	204 90 isoforms
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	205 88 TSS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	206 0 CDS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	207 87 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	208 88 splicing
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	209 0 relCDS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	210 > sink("cuffdb_info.txt")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	211 > print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	212 > print("SAMPLES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	213 > samples(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	214 > print("REPLICATES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	215 > replicates(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	216 > print("FEATURES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	217 > print(annotation(genes(cuff)))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	218 > cat(annotation(genes(cuff))[[1]],sep=",")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	219 > sink()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	220 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	221 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	222 > tryCatch({
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	223 + if (args$plotType == 'density') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	224 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	225 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	226 + else if (args$plotType == 'boxplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	227 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	228 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	229 + else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	230 + MDSplot(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	231 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	232 + else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	233 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	234 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	235 + else if (args$plotType == 'dendrogram') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	236 + csDendro(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	237 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	238 + else if (args$plotType == 'scatter') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	239 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	240 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	241 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	242 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	243 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	244 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	245 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	246 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	247 + else if (args$plotType == 'volcano') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	248 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	249 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	250 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	251 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	252 + myGenes <- genes(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	253 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	254 + csVolcano(myGenes, args$x, args$y)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	255 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	256 + else if (args$plotType == 'heatmap') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	257 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	258 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	259 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	260 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	261 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	262 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	263 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	264 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	265 + else if (args$plotType == 'cluster') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	266 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	267 + csCluster(get_features(myGenes, args$features), k=args$k)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	268 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	269 + else if (args$plotType == 'dispersion') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	270 + dispersionPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	271 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	272 + else if (args$plotType == 'fpkmSCV') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	273 + fpkmSCVPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	274 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	275 + else if (args$plotType == 'scatterMatrix') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	276 + csScatterMatrix(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	277 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	278 + else if (args$plotType == 'expressionplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	279 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	280 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	281 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	282 + else if (args$plotType == 'expressionbarplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	283 + myGeneId <- args$genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	284 + myGenes <- getGenes(cuff, myGeneId)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	285 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	286 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	287 + else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	288 + MDSplot(genes(cuff),replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	289 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	290 + else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	291 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	292 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	293 + else if (args$plotType == 'maplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	294 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	295 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	296 + else if (args$plotType == 'genetrack') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	297 + myGene <- getGene(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	298 + plotTracks(makeGeneRegionTrack(myGene))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	299 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	300 + },error = function(e) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	301 + write(paste("Failed:", e, sep=" "), stderr())
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	302 + q("no", 1, TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	303 + })
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	304 Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	305 geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	306 Fontconfig error: Cannot load default config file
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	307 Warning message:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	308 In .local(object, FPKMLowerBound, ...) :
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	309 At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	310 > devname = dev.off()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	311 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	312 > #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	313 >

Mercurial > repos > devteam > cummerbund

annotate test-data/fpkmSCV.txt @ 4:ba8fde59843d draft