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comparison chipseeker.R @ 6:b418a1d3585d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
author rnateam
date Wed, 13 Mar 2019 03:05:16 -0400
parents 90fe78a19b55
children 1b9a9409831d
comparison
equal deleted inserted replaced
5:4c2dbe4dbb4e 6:b418a1d3585d
15 make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."), 15 make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."),
16 make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"), 16 make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"),
17 make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"), 17 make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"),
18 make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"), 18 make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"),
19 make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"), 19 make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"),
20 make_option(c("-j","--ignoreUpstream"), type="logical", help="Ignore upstream"),
21 make_option(c("-k","--ignoreDownstream"), type="logical", help="Ignore downstream"),
20 make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."), 22 make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."),
21 make_option(c("-p","--plots"), type="logical", help="PDF of plots."), 23 make_option(c("-p","--plots"), type="logical", help="PDF of plots."),
22 make_option(c("-r","--rdata"), type="logical", help="Output RData file.") 24 make_option(c("-r","--rdata"), type="logical", help="Output RData file.")
23 ) 25 )
24 26
29 gtf = args$gtf 31 gtf = args$gtf
30 up = args$upstream 32 up = args$upstream
31 down = args$downstream 33 down = args$downstream
32 format = args$format 34 format = args$format
33 35
36 if (!is.null(args$flankgeneinfo)) {
37 flankgeneinfo <- TRUE
38 } else {
39 flankgeneinfo <- FALSE
40 }
41
42 if (!is.null(args$ignoreUpstream)) {
43 ignoreUpstream <- TRUE
44 } else {
45 ignoreUpstream <- FALSE
46 }
47
48 if (!is.null(args$ignoreDownstream)) {
49 ignoreDownstream <- TRUE
50 } else {
51 ignoreDownstream <- FALSE
52 }
53
34 peaks <- readPeakFile(peaks) 54 peaks <- readPeakFile(peaks)
35 55
36 # Make TxDb from GTF 56 # Make TxDb from GTF
37 txdb <- makeTxDbFromGFF(gtf, format="gtf") 57 txdb <- makeTxDbFromGFF(gtf, format="gtf")
38 if (!is.null(args$flankgeneinfo)) { 58
39 peakAnno <- annotatePeak(peaks, TxDb=txdb, tssRegion=c(-up, down), addFlankGeneInfo=args$flankgeneinfo, flankDistance=args$flankgenedist) 59 # Annotate peaks
40 } else { 60 peakAnno <- annotatePeak(peaks, TxDb=txdb,
41 peakAnno <- annotatePeak(peaks, TxDb=txdb, tssRegion=c(-up, down)) 61 tssRegion=c(-up, down),
42 } 62 addFlankGeneInfo=flankgeneinfo,
63 flankDistance=args$flankgenedist,
64 ignoreUpstream=ignoreUpstream,
65 ignoreDownstream=ignoreDownstream)
43 66
44 # Add gene name 67 # Add gene name
45 features <- import(gtf, format="gtf") 68 features <- import(gtf, format="gtf")
46 ann <- unique(mcols(features)[, c("gene_id", "gene_name")]) 69 ann <- unique(mcols(features)[, c("gene_id", "gene_name")])
47 res <- as.data.frame(peakAnno) 70 res <- as.data.frame(peakAnno)