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comparison diffbind.R @ 15:194e3f2c1d86 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
author iuc
date Tue, 09 Jul 2019 18:46:09 -0400
parents 1de83981d43c
children 163688bb8f73
comparison
equal deleted inserted replaced
14:c97a786e8fb5 15:194e3f2c1d86
55 sampleTable <- data.frame(SampleID=samples, 55 sampleTable <- data.frame(SampleID=samples,
56 Condition=groups, 56 Condition=groups,
57 bamReads=bams, 57 bamReads=bams,
58 bamControl=ctrls, 58 bamControl=ctrls,
59 Peaks=peaks, 59 Peaks=peaks,
60 Tissue=samples, # using "Tissue" column to display ids as labels in PCA plot 60 Tissue=samples) # using "Tissue" column to display ids as labels in PCA plot
61 stringsAsFactors=FALSE)
62 } else { 61 } else {
62
63 sampleTable <- data.frame(SampleID=samples, 63 sampleTable <- data.frame(SampleID=samples,
64 Replicate=samples, 64 Replicate=samples,
65 Condition=groups, 65 Condition=groups,
66 bamReads=bams, 66 bamReads=bams,
67 Peaks=peaks, 67 Peaks=peaks,
68 Tissue=samples, 68 Tissue=samples)
69 stringsAsFactors=FALSE)
70 } 69 }
71 70
72 sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter) 71 sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter)
73 72
74 if ( !is.null(opt$summits) ) { 73 if ( !is.null(opt$summits) ) {
124 Name=rep("DiffBind", length(resSorted)), 123 Name=rep("DiffBind", length(resSorted)),
125 Score=rep("0", length(resSorted)), 124 Score=rep("0", length(resSorted)),
126 Strand=gsub("\\*", ".", strand(resSorted)), 125 Strand=gsub("\\*", ".", strand(resSorted)),
127 mcols(resSorted)) 126 mcols(resSorted))
128 } 127 }
129 write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE) 128 write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, row.names = FALSE)
130 129
131 # Output binding affinity scores 130 # Output binding affinity scores
132 if (!is.null(opt$bmatrix)) { 131 if (!is.null(opt$bmatrix)) {
133 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) 132 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
134 # Output as 0-based tabular 133 # Output as 0-based tabular