Mercurial > repos > kpbioteam > ewastools

comparison minfi_dmp.xml @ 64:3d083550977f draft

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Uploaded
author kpbioteam
date Thu, 04 Apr 2019 11:21:19 -0400
parents cffa2871fe8b
children 53aaf097238c
comparison
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63:2ee6ac5227f1 64:3d083550977f
27 27
28 tab <- read.table('$ucsc_genome') 28 tab <- read.table('$ucsc_genome')
29 29
30 tab <- tab[,-(11:14),drop=FALSE] 30 tab <- tab[,-(11:14),drop=FALSE]
31 31
32 colnames(tab) <- c("seqname","source","feature","start","end","score","strand", "frame","attributes", "names") 32 tab <- tab[,c(1,4,5,10)]
33 33
34 tab[,"source"] <- NULL 34 colnames(tab) <- c('chr','start','end','names')
35
36 tab[,"frame"] <- NULL
37
38 tab[,"attributes"] <- NULL
39 35
40 dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar) 36 dmp <- dmpFinder(beta, pheno[,"V2"], type = type, qCutoff = qCutoff, shrinkVar = shrinkVar)
41 37
42 dmp[,"names"] <- rownames(dmp) 38 dmp[,"names"] <- rownames(dmp)
43 39
44 data <- merge(dmp, tab, by="names",sort = TRUE) 40 data <- merge(dmp, tab, by="names",sort = TRUE)
45 41
46 data <- data[c("seqname","start","end","names","score","strand", "feature","intercept", "f", "pval","qval")] 42 data <- data[,c(6,7,8,1,4,5)]
47 43
48 write.table(data, file= '$dmp', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t") 44 write.table(data, file= '$dmp', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t")
49 ]]> 45 ]]>
50 </configfile> 46 </configfile>
51 </configfiles> 47 </configfiles>
52 <inputs> 48 <inputs>
53 <param type="data" name="grset" format="rdata" label="Input Set" help="MethylSet, RatioSet or GenomicRatioSet" /> 49 <param type="data" name="grset" format="rdata" label="Input Set" help="MethylSet, RatioSet or GenomicRatioSet" />
54 <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"/> 50 <param type="data" name="phenotype_table" format="tabular" label="Phenotype Table"/>
55 <param name="phenotype" type="select" label="Phenotype Type"> 51 <param name="phenotype" type="select" label="Phenotype Type">
56 <option value="categorical">categorical</option> 52 <option value="categorical">categorical</option>
57 <option value="continuous">continuous</option> 53 <option value="continuous">continuous</option>
58 </param> 54 </param>
59 <param name="q_cutoff" type="integer" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/> 55 <param name="q_cutoff" type="float" value="1" label="qCutoff Size" help="DMPs with an FDR q-value greater than this will not be returned."/>
60 <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage" 56 <param name="variance_shrinkage" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Variance Shrinkage"
61 help="Enable variance shrinkage is recommended when sample sizes are small"/> 57 help="Enable variance shrinkage is recommended when sample sizes are small"/>
62 <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/> 58 <param type="data" name="ucsc_genome" format="gtf" label="Genome Table" help="UCSC genome data Methyl450"/>
63 </inputs> 59 </inputs>
64 <outputs> 60 <outputs>
65 <data name="dmp" format="interval" label="Differentially Methylated Positions"/> 61 <data name="dmp" format="interval" label="Differentially Methylated Positions"/>
66 </outputs> 62 </outputs>
67 <tests> 63 <tests>
68 <test> 64 <test>
69 <param name="grset" value="GRSet_without_SNPs.rdata"/> 65 <param name="grset" value="GRSet_without_SNPs.rdata"/>
70 <param name="phenotype_table" value="phenotypeTable.txt"/> 66 <param name="phenotype_table" value="phenotypeTable.txt"/>
78 <help><![CDATA[ 74 <help><![CDATA[
79 This tool creates differentially methylated positions (DMPs) with respect to a phenotype covariate. The phenotype may be categorical (e.g. cancer vs. normal) or continuous (e.g. blood pressure). 75 This tool creates differentially methylated positions (DMPs) with respect to a phenotype covariate. The phenotype may be categorical (e.g. cancer vs. normal) or continuous (e.g. blood pressure).
80 76
81 The output is an interval file with the following columns: 77 The output is an interval file with the following columns:
82 78
83 - seqnames 79 - chr
84 - start 80 - start
85 - end 81 - end
86 - cpg
87 - names 82 - names
88 - score 83 - pvalue
89 - strand 84 - qval
90 - feature
91 - intercept
92 - f pval
93 - qval
94 85
95 ]]></help> 86 ]]></help>
96 <expand macro="citations" /> 87 <expand macro="citations" />
97 </tool> 88 </tool>