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comparison diffbind.R @ 7:fa67bcb732f6 draft

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Uploaded
author bgruening
date Tue, 14 Jan 2014 05:04:34 -0500
parents 8d48d5591389
children 20c431b4cf74
comparison
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6:da65ae70e2e1 7:fa67bcb732f6
8 args <- commandArgs(trailingOnly = TRUE) 8 args <- commandArgs(trailingOnly = TRUE)
9 9
10 #get options, using the spec as defined by the enclosed list. 10 #get options, using the spec as defined by the enclosed list.
11 #we read the options from the default: commandArgs(TRUE). 11 #we read the options from the default: commandArgs(TRUE).
12 spec = matrix(c( 12 spec = matrix(c(
13 'verbose', 'v', 2, "integer", 13 'verbose', 'v', 2, "integer",
14 'help' , 'h', 0, "logical", 14 'help' , 'h', 0, "logical",
15 'outfile' , 'o', 1, "character", 15 'outfile' , 'o', 1, "character",
16 'plots' , 'p', 2, "character", 16 'plots' , 'p', 2, "character",
17 'infile' , 'i', 1, "character", 17 'infile' , 'i', 1, "character",
18 'format', 'f', 1, 'character', 18 'format', 'f', 1, 'character'
19 ), byrow=TRUE, ncol=4); 19 ), byrow=TRUE, ncol=4);
20
20 opt = getopt(spec); 21 opt = getopt(spec);
21 22
22 # if help was asked for print a friendly message 23 # if help was asked for print a friendly message
23 # and exit with a non-zero error code 24 # and exit with a non-zero error code
24 if ( !is.null(opt$help) ) { 25 if ( !is.null(opt$help) ) {
25 cat(getopt(spec, usage=TRUE)); 26 cat(getopt(spec, usage=TRUE));
26 q(status=1); 27 q(status=1);
27 } 28 }
28 29
29 30
30 library(DiffBind) 31 library('DiffBind')
31 # used to save to BED, GFF or WIG format 32 # used to save to BED, GFF or WIG format
32 library(rtracklayer) 33 library('rtracklayer')
33 34
34 if ( !is.null(opt$plots) ) { 35 if ( !is.null(opt$plots) ) {
35 pdf(opt$plots) 36 pdf(opt$plots)
36 } 37 }
37 38