genepattern2spd: GenePattern to SPD

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

Convert from GenePattern GCT and CLS files to the input file required for Sample Progression Discovery (SPD) The input file is a matlab binary file, containing probe names, data matrix and samples names, and optionally class labels, from a cls file. This makes use of the R.matlab library by Henrik Bengtsson & creates v5 matlab files (which work fine with matlab v7.)

Usage

genepattern2spd(gct.file, cls.files, cls.names = "Class",
  out.file = "spd.mat")

Arguments

gct.file	The path to a GenePattern formatted GCT file
cls.files	The path to a GenePattern formatted CLS file. Optional.
cls.names	What do the classes in cls.file represent? Tumour Type? Cell Line? Specify a short label, eg “Tumour Type”
out.file	The path to the output file. It should end in .mat.

Value

Creates a version 5 matlab file which you can then open in Matlab

TODO

support >1 cls files

Author(s)

Mark Cowley, 2011-04-20

See Also

http://icbp.stanford.edu/software/SPD, http://www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_fileformats.html#gct, http://www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_fileformats.html#cls

Examples

## Not run: 
setwd("/Volumes/marcow-1/projects/SPD/analysisV1")
genepattern2spd("norm.rsn.medianNorm.gct", out.file="norm.rsn.medianNorm.SPD.mat")
genepattern2spd("norm.rsn.medianNorm.gct", "norm.rsn.medianNorm.cls", "Tumour Grade", "norm.rsn.medianNorm.SPD.mat")

## End(Not run)

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.