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1 #!/usr/bin/env Rscript
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2 argspec <- c("tab.2.cdt.R converts a data matrix to cdt format
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3
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4 Usage:
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5 tab.2.cdt.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
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16 lib.load.quiet <- function( package ) {
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17 package <- as.character(substitute(package))
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18 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
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19 }
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20 lib.load.quiet(getopt)
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21
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22
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23 spec <- matrix( c( "data.fname", "d", 1, "character",
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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 if ( is.null( opt$output.fname ) ) opt$output.fname <- sub( "tab$|csv$", "cdt", opt$data.fname )
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32
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33 cl <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
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34 cl <- cl[,1]
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35 save( file=opt$output.fname, cl )
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