Mercurial > repos > bgruening > diffbind

comparison diffbind.R @ 13:1de83981d43c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
author iuc
date Wed, 30 May 2018 12:25:42 -0400
parents 4c7ab9995f9e
children 194e3f2c1d86
comparison
equal deleted inserted replaced
12:fa56d93f7980 13:1de83981d43c
92 dev.off() 92 dev.off()
93 } 93 }
94 94
95 # Output differential binding sites 95 # Output differential binding sites
96 resSorted <- diff_bind[order(diff_bind$FDR),] 96 resSorted <- diff_bind[order(diff_bind$FDR),]
97 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE) 97 # Convert from GRanges (1-based) to 0-based format (adapted from https://www.biostars.org/p/89341/)
98 if (opt$format == "bed") {
99 resSorted <- data.frame(Chrom=seqnames(resSorted),
100 Start=start(resSorted) - 1,
101 End=end(resSorted),
102 Name=rep("DiffBind", length(resSorted)),
103 Score=rep("0", length(resSorted)),
104 Strand=gsub("\\*", ".", strand(resSorted)))
105 } else if (opt$format == "interval") {
106 # Output as interval
107 df <- as.data.frame(resSorted)
108 extrainfo <- NULL
109 for (i in 1:nrow(df)) {
110 extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse="|")
111 }
112 resSorted <- data.frame(Chrom=seqnames(resSorted),
113 Start=start(resSorted) - 1,
114 End=end(resSorted),
115 Name=rep("DiffBind", length(resSorted)),
116 Score=rep("0", length(resSorted)),
117 Strand=gsub("\\*", ".", strand(resSorted)),
118 Comment=extrainfo)
119 } else {
120 # Output as 0-based tabular
121 resSorted <- data.frame(Chrom=seqnames(resSorted),
122 Start=start(resSorted) - 1,
123 End=end(resSorted),
124 Name=rep("DiffBind", length(resSorted)),
125 Score=rep("0", length(resSorted)),
126 Strand=gsub("\\*", ".", strand(resSorted)),
127 mcols(resSorted))
128 }
129 write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE)
98 130
99 # Output binding affinity scores 131 # Output binding affinity scores
100 if (!is.null(opt$bmatrix)) { 132 if (!is.null(opt$bmatrix)) {
101 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) 133 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
102 write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE) 134 # Output as 0-based tabular
135 bmat <- data.frame(Chrom=bmat[, 1],
136 Start=bmat[, 2] - 1,
137 End=bmat[, 3],
138 bmat[, 4:ncol(bmat)])
139 write.table(bmat, file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE)
103 } 140 }
104 141
105 # Output RData file 142 # Output RData file
106 if (!is.null(opt$rdaOpt)) { 143 if (!is.null(opt$rdaOpt)) {
107 save.image(file = "DiffBind_analysis.RData") 144 save.image(file = "DiffBind_analysis.RData")