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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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3
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15 ## some helper fn's
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16 write.2.tab <- function( mat,
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17 fname ) {
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18 mat <- rbind( colnames( mat ), mat )
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19 mat <- cbind( c( "ID", rownames( mat )[-1] ),
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20 mat )
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21 write.table( mat, fname, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE )
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22 }
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23 lib.load.quiet <- function( package ) {
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24 package <- as.character(substitute(package))
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25 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
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26 }
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27 lib.load.quiet(getopt)
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28
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29 spec <- matrix( c( "data.fname", "d", 1, "character",
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3
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30 "output.fname", "o", 2, "character",
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31 "return.normals", "r", 2, "character",
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32 "out.norm.fname", "O", 2, "character"
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33 ),
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34 nc=4,
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35 byrow=TRUE
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36 )
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37
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38 opt <- getopt( spec=spec )
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39 if ( is.null( opt$output.fname ) ) { opt$output.fname <- 'merge_merge.tumors.tab' }
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3
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40 if ( is.null( opt$return.normals ) ) {
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41 opt$return.normals <- FALSE
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42 } else {
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43 opt$return.normals <- ( tolower( opt$return.normals ) %in% "yes" )
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44 }
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45 if ( is.null( opt$out.norm.fname ) ) { opt$out.norm.fname <- 'merge_merge.normals.tab' }
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46
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47 mat <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
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3
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48 norms <- matrix( NA, nc=0, nr=nrow( mat ), dimnames=list( rownames( mat ), c() ) )
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49 if ( length( strsplit( colnames( mat ), "-" )[[1]] ) > 3 ) {
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50 cnames <- sapply( strsplit( colnames( mat ), "-" ), function(x) x[4] )
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51 norms <- grepl( "^1", cnames )
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52
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53 if ( sum( norms ) > 0 ) {
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54 tumors <- ! norms
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55 norms <- mat[, norms ]
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56 mat <- mat[, tumors ]
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57 }
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3
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58 } else {
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59 if ( opt$return.normals ) {
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60 writeLines( "TCGA ID barcodes in supplied file only provide patient sample info (no aliquot components are in IDs)\n", opt$out.norm.fname )
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61 }
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62 }
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63 write.2.tab( mat, opt$output.fname )
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64 if ( opt$return.normals ) {
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65 if ( ncol( norms ) > 0 ) {
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66 write.2.tab( norms, opt$out.norm.fname )
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67 } else {
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68 writeLines( "no normals found in supplied matrix\n", opt$out.norm.fname )
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69 }
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70 }
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