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revision 1.1, Mon Apr 19 20:22:16 2010 UTC revision 1.2, Fri Jan 7 22:20:38 2011 UTC
# Line 31  Line 31 
31  }  }
32    
33  args = commandArgs(TRUE);  args = commandArgs(TRUE);
34  if (length(args) != 2) { print("usage:  Rscript SplitGeneSets.R gene_sets pearson_cutoff"); q() }  if (length(args) != 3) { print("usage:  Rscript SplitGeneSets.R gene_sets pearson_cutoff output_dir"); q() }
35  gene_sets_file = args[1];  gene_sets_file = args[1];
36  splitting_cutoff = as.numeric(args[2]);  splitting_cutoff = as.numeric(args[2]);
37    output_dir = args[3];
38    
39  ## Read in gene expression data ##  ## Read in gene expression data ##
40  ## This file is the output of 'exprs' from Bioconductor's RMA procedure  ## This file is the output of 'exprs' from Bioconductor's RMA procedure
41  ## Header line contains experiment names  ## Header line contains experiment names
42  ## row name is gene id, rest of the columns are normalized expression values per experiment  ## row name is gene id, rest of the columns are normalized expression values per experiment
43  all_geneexp=as.matrix(read.table("raw_data.tab",header=TRUE));  all_geneexp=as.matrix(read.table(paste(output_dir, "rma_normalized.tab", sep="/"),header=TRUE));
44  num_genes = dim(all_geneexp)[1];  num_genes = dim(all_geneexp)[1];
45  num_experiments = dim(all_geneexp)[2];  num_experiments = dim(all_geneexp)[2];
46    

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