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1 #!/usr/bin/env Rscript
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2 argspec <- c("fix.and.merge.TCGA.samples.IDs.R takes a clustering from ConsensusClusterPlus and clinical survival data
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3 and generates a KM-plot, along with the log-rank p-values
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4
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5 Usage:
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6 fix.and.merge.TCGA.samples.IDs.R -d <data.file>
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7
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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 "num.components", "n", 2, "integer",
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23 "remove.normals", "r", 0, "logical",
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24 "output.fname", "o", 2, "character"
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25 ),
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26 nc=4,
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27 byrow=TRUE
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28 )
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29
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30 opt <- getopt( spec=spec )
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31
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32 data <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
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33 if ( is.null( opt$num.components ) ) { opt$num.components <- 3 }
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34 if ( is.null( opt$remove.normals ) ) { opt$remove.normals <- FALSE }
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35 if ( is.null( opt$output.fname ) ) { opt$output.fname <- paste( "sample.IDs.updated", basename( opt$data.fname ), sep="." ) }
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36
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37 if ( opt$num.components < 3 ) {
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38 err.msg <- "Minimum number of barcode components that can be used is 3\n"
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39 cat( err.msg, file=opt$output.fname )
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40 stop( err.msg )
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41 }
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42
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43 remove.periods.from.ids <- function( ids ) {
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44 return( gsub( "\\.", "-", ids ) )
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45 }
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46
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47
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48 reformat.ids <- function( ids,
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49 num.components=3 ) {
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50 return( sapply( strsplit( ids, "-" ), function(x) paste( x[1:num.components], collapse="-" ) ) )
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51 }
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52
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53
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54 merge.cols <- function( mat,
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55 samp.ids ) {
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56
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57 if ( ! any( duplicated( samp.ids ) ) ) {
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58 colnames( mat ) <- samp.ids
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59 return( mat )
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60 }
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61
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62 dupes <- unique( samp.ids[ duplicated( samp.ids ) ] )
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63 uniqs <- samp.ids[ ! samp.ids %in% dupes ]
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64
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65 uniq.mat <- mat[ , ( samp.ids %in% uniqs ), drop=FALSE ]
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66 colnames( uniq.mat ) <- uniqs
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67
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68 for ( dup in dupes ) {
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69 dup.mat <- apply( mat[, ( samp.ids %in% dup ), drop=FALSE],
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70 1,
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71 mean,
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72 na.rm=TRUE )
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73
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74 uniq.mat <- cbind( uniq.mat, dup.mat )
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75 }
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76 colnames( uniq.mat ) <- c( uniqs, dupes )
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77 return( uniq.mat )
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78 }
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79
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80
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81 cnames <- colnames( data )
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82 rnames <- rownames( data )
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83
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84 transpose.back <- FALSE
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85
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86 if ( all( grepl( "^TCGA", rnames ) ) ) {
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87 data <- t( data )
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88 transpose.back <- TRUE
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89 } else {
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90 if ( ! all( grepl( "^TCGA", cnames ) ) ) {
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91 err.msg <- "can't find any TCGA samples listed in this matrix. If columns are samples, all columns must be a TCGA sample ID. Same if rows are samples.\n"
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92 cat( err.msg, file=opt$output.fname )
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93 stop( err.msg )
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94 }
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95 }
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96
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97 cnames <- remove.periods.from.ids( colnames( data ) )
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98 nelts <- as.numeric( names( table( as.factor( sapply( strsplit( cnames, "-" ), function(x) length(x ) ) ) ) ) )
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99 if ( length( nelts ) > 1 ) {
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100 err.msg <- "Error: Inconsistent TCGA sample barcodes used. Have found ID with different numbers of components in the barcodes used\n"
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101 cat( err.msg, file=opt$output.fname )
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102 stop( err.msg )
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103 }
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104
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105 if ( opt$remove.normals ) {
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106 if ( nelts > 3 ) {
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107 normals <- grepl( "^TCGA-..-....-1", cnames )
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108 data <- data[ , (! normals ), drop=FALSE ]
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109 }
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110 }
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111
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112 if ( opt$num.components < nelts ) {
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113 cnames <- reformat.ids( ids=cnames, num.components=opt$num.components )
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114 data <- merge.cols( data, cnames )
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115 }
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116
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117 if ( transpose.back ) data <- t( data )
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118
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119 write.table( data, opt$output.fname, sep="\t", quote=FALSE, col.names=NA )
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