import.gsea.res: Import a GenePattern res file

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

Description

res files contain 2 columns per sample: a Signal, and a Call column, where Call contains a detection call - either a P/M/A, or a proabability. These calls can be imported, or thrown away via the calls parameter.

Usage

import.gsea.res(f, calls = TRUE)

Arguments

f	the path to a res file
calls	logical: if TRUE, retain the detection calls, if FALSE, throw away Calls, and rename Signal columns to strip out the trailing “.Signal”

Value

a data.frame of usually gene expression data. columns 1&2 are annotation, 3+ are data, in alternating pairs of Signal and Calls... ie 2n+2 columns in total. If calls=TRUE, ncol=2+N, if calls=FALSE, ncol=2+2N

Author(s)

Mark Cowley, 2009-07-27

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