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1 #!/usr/bin/env Rscript
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2 argspec <- c("remove.degenerate.values.R replaces degenerate values (NaNs & Infs) with a user-specified value
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3
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4 Usage:
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5 remove.degenerate.values.R -d <data.file>
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6 Optional:
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7 -r <replacement_value> (default is NA)
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8 -o <output_file>
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9 \n\n")
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10 args <- commandArgs(TRUE)
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11 if ( length( args ) == 1 && args =="--help") {
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12 write(argspec, stderr())
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13 q();
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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 spec <- matrix( c( "data.fname", "d", 1, "character",
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23 "replacement.val", "r", 2, "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
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32 data <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
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33 if ( is.null( opt$replacement.val ) ) { opt$replacement.val <- NA }
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34 if ( ! is.null( opt$replacement.val ) ) { opt$replacement.val <- as.integer( opt$replacement.val ) }
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35 if ( is.null( opt$output.fname ) ) { opt$output.fname <- paste( "degenerate.vals.replaced", basename( opt$data.fname ), sep="." ) }
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36
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37 ## Set any NA, NAN or Inf entries to 0
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38 if ( any(is.nan(data)) ) data[ is.nan( data ) ] <- opt$replacement.val
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39 if ( any(is.infinite(data)) ) data[ is.infinite( data ) ] <- opt$replacement.val
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40
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41 write.table( data, opt$output.fname, sep="\t", quote=FALSE, col.names=NA )
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