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