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1 #!/usr/bin/env Rscript
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2 argspec <- c("remove.tcga.normals.R removes TCGA normal samples from a given matrix
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3
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4 Usage:
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5 remove.tcga.normals.R -d <data.file>
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6 Optional:
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7 -o <output_file>
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8 \n\n")
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9 args <- commandArgs(TRUE)
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10 if ( length( args ) == 1 && args =="--help") {
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11 write(argspec, stderr())
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12 q();
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13 }
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14
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15 lib.load.quiet <- function( package ) {
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16 package <- as.character(substitute(package))
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17 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
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18 }
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19 lib.load.quiet(getopt)
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20
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21 spec <- matrix( c( "data.fname", "d", 1, "character",
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22 "output.fname", "o", 2, "character"
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23 ),
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24 nc=4,
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25 byrow=TRUE
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26 )
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27
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28 opt <- getopt( spec=spec )
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29 if ( is.null( opt$output.fname ) ) { opt$output.fname <- 'merge_merge.tumors.tab' }
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30
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31 mat <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
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32 if ( length( strsplit( colnames( mat ), "-" )[[1]] ) == 4 ) {
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33 cnames <- sapply( strsplit( colnames( mat ), "-" ), function(x) x[4] )
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34 norms <- grepl( "^1", cnames )
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35
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36 if ( sum( norms ) > 0 ) {
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37 tumors <- ! norms
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38 mat <- mat[, tumors ]
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39 }
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40 }
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41 write.table( mat, opt$output.fname, quote=FALSE, sep="\t", col.names=NA )
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