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1 #!/usr/bin/env Rscript
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2 ## Script by Peter Waltman
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3 ##
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4 ## License under Creative Commons Attribution 3.0 Unported (CC BY 3.0)
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5 ##
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6 argspec <- c("TBD
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7
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8
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9 Usage:
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10 normalize.matrix.R -d <data.file>
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11 Optional:
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12 -o <output.name>
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13 TBD
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14 \n\n")
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15
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16 args <- commandArgs(TRUE)
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17 if ( length( args ) == 1 && args =="--help") {
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18 write(argspec, stderr())
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19 q();
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20 }
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21
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1
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22 ## some helper fn's
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23 write.2.tab <- function( mat,
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24 fname ) {
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25 mat <- rbind( colnames( mat ), mat )
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26 mat <- cbind( c( "ID", rownames( mat )[-1] ),
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27 mat )
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28 write.table( mat, fname, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE )
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29 }
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30
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31 lib.load.quiet <- function( package ) {
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32 package <- as.character(substitute(package))
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33 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
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34 }
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35 lib.load.quiet(getopt)
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36
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37
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38 spec <- matrix( c( "data.fname", "d", 1, "character",
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39 "center.rows", "r", 2, "character",
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40 "var.adj.rows", "R", 2, "character",
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41 "center.cols", "c", 2, "character",
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42 "var.adj.cols", "C", 2, "character",
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43 "output.fname", "o", 2, "character"
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44 ),
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45 nc=4,
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46 byrow=TRUE
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47 )
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48
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49 opt <- getopt( spec=spec )
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50
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51 #set some reasonable defaults for the options that are needed,
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52 #but were not specified.
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53 if ( is.null( opt$output.fname ) ) {
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54 out.fname <- ""
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55 if ( ! is.null( opt$center.rows ) ) out.fname <- paste( "row", opt$center.rows, "centered", out.fname, sep="." )
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56 if ( ! is.null( opt$center.cols ) ) out.fname <- paste( "col", opt$center.cols, "centered", out.fname, sep="." )
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57 if ( ! is.null( opt$var.adj.rows ) ) out.fname <- paste( "row", opt$var.adj.rows, "var.adjed", out.fname, sep="." )
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58 if ( ! is.null( opt$var.adj.cols ) ) out.fname <- paste( "col", opt$var.adj.cols, "var.adjed", out.fname, sep="." )
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59
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60 opt$output.fname <- paste( out.fname, "centered.matrix", sep="." )
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61 }
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62 if ( is.null( opt$center.rows ) ) { opt$center.rows <- 'none' }
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63 if ( is.null( opt$center.cols ) ) { opt$center.cols <- 'none' }
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64 if ( is.null( opt$var.adj.rows ) ) { opt$var.adj.rows <- 'none' }
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65 if ( is.null( opt$var.adj.cols ) ) { opt$var.adj.cols <- 'none' }
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66
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67 data <- as.matrix( read.delim( opt$data.fname, header=T, row.names=1 , check.names=FALSE ) )
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68 my.center <- rep( 0, nrow( data ) )
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69 my.var.adj <- rep( 1, nrow( data ) )
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70 if ( opt$center.rows != "none" ) {
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71 my.center.fn <- get( opt$center.rows )
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72 ##data <- sweep( data, 1, apply( data, 1, my.center.fn, na.rm=T ) )
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73 my.center <- apply( data, 1, my.center.fn, na.rm=T )
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74 }
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75 if ( opt$var.adj.rows != "none" ) {
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76 my.var.adj.fn <- get( opt$var.adj.rows )
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77 my.var.adj <- apply( data, 1, my.var.adj.fn, na.rm=T )
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78 }
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79 data <- t( scale( t( data ), center=my.center, scale=my.var.adj ) )
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80
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1
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81 my.center <- rep( 0, ncol( data ) )
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82 my.var.adj <- rep( 1, ncol( data ) )
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83 if ( opt$center.cols != "none" ) {
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84 my.center.fn <- get( opt$center.cols )
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85 ##data <- sweep( data, 2, apply( data, 2, my.center.fn, na.rm=T ) )
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86 my.center <- apply( data, 2, my.center.fn, na.rm=T )
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87 }
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88 my.var.adj <- rep( 1, ncol( data ) )
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89 if ( opt$var.adj.cols != "none" ) {
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90 my.var.adj.fn <- get( opt$var.adj.cols )
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91 my.var.adj <- apply( data, 2, my.var.adj.fn, na.rm=T )
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92 }
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93 data <- scale( data, center=my.center, scale=my.var.adj )
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94
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1
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95 write.2.tab( data, opt$output.fname )
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96
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