changeset 5:cbc3ecce98ee draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/normalize.matrix.by.other.R	Fri Mar 01 19:53:49 2013 -0500
@@ -0,0 +1,84 @@
+#!/usr/bin/env Rscript
+##  Script by Peter Waltman
+## 
+## License under Creative Commons Attribution 3.0 Unported (CC BY 3.0)
+##
+argspec <- c("TBD
+
+
+        Usage: 
+                normalize.matrix.R -d <data.file> 
+        Optional:
+                -o <output.name>
+                TBD 
+                \n\n")
+
+args <- commandArgs(TRUE)
+if ( length( args ) == 1 && args =="--help") { 
+  write(argspec, stderr())
+  q();
+}
+
+## some helper fn's
+write.2.tab <- function( mat,
+                         fname ) {
+  mat <- rbind( colnames( mat ), mat )
+  mat <- cbind( c( "ID", rownames( mat )[-1] ),
+                      mat )
+  write.table( mat, fname, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE )
+}
+
+lib.load.quiet <- function( package ) {
+   package <- as.character(substitute(package))
+   suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
+}
+lib.load.quiet(getopt)
+
+
+spec <- matrix( c( "data.fname",         "d", 1, "character",
+                   "data.fname2",        "D", 1, "character",
+                   "ctr.method",         "c", 2, "character",
+                   "output.fname",       "o", 2, "character",
+                   "return.normals",     "r", 2, "character",
+                   "out.norm.fname",     "O", 2, "character"
+                   ),
+                nc=4,
+                byrow=TRUE
+               )
+
+opt <- getopt( spec=spec )
+
+#set some reasonable defaults for the options that are needed,
+#but were not specified.
+if ( is.null( opt$output.fname ) ) { opt$output.fname <- 'merge_merge.tumors.tab' }
+if ( is.null( opt$ctr.method ) ) { opt$ctr.method <- 'median' }
+if ( is.null( opt$return.normals ) ) {
+  opt$return.normals <- FALSE
+} else {
+  opt$return.normals <- ( tolower( opt$return.normals ) %in% "yes" )
+}
+if ( is.null( opt$out.norm.fname ) ) { opt$out.norm.fname <- 'merge_merge.normals.tab' }
+
+
+data <- as.matrix( read.delim( opt$data.fname, header=T, row.names=1 , check.names=FALSE ) )
+normer.data <- as.matrix( read.delim( opt$data.fname2, header=T, row.names=1 , check.names=FALSE ) )
+if ( ! all( rownames(data) %in% rownames(normer.data) ) ) {
+  gene.ovp <- rownames(data)
+  gene.ovp <- gene.ovp[ gene.ovp %in% rownames(normer.data) ]
+  if ( length( gene.ovp ) == 0 ) stop( 'No gene overlap between specified matrices\n' )
+
+  data <- data[ gene.ovp, , drop=F ]
+  normer.data <- normer.data[ gene.ovp, , drop=F ]
+}
+
+my.ctr.vals <- apply( normer.data, 1, get( opt$ctr.method ), na.rm=T )
+
+data <- apply( data, 2, function(x) x-my.ctr.vals )
+
+write.2.tab( data, opt$output.fname )
+if ( opt$return.normals ) {
+  normer.data <- normer.data - my.ctr.vals
+  write.2.tab( normer.data, opt$out.norm.fname )
+}
+
+