gsea.gct.probes2genes: Convert probe-level to gene-level gct

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

Description

Take a table of expression data (at the probe-level), and convert it to a table of expression data at the unique gene-symbol-level. This chooses the best probe for each gene by looking at the stats vector which should be equivalent to the contents of a rnk file (todo: allow a rnk file to be specified) There's 2 ways of chooseing the best probe - Mark's way (Best_probe), or the default GSEA way which is called "Max_probe".

Usage

gsea.gct.probes2genes(data, stats, chip, mode = c("Best_probe", "Max_probe",
  "Median_of_probes"))

Arguments

data	a data.frame of expression data
stats	a vector of statistics
chip	either the filename of a chip file, or the result of import.gsea.chip
mode	“Best_probe” or “Max_probe”

Value

a data.frame of expression data with 1 row per unique gene symbol, and gene symbols as the rownames see also gsea.genesets2gct.

Author(s)

Mark Cowley, 2009-07-27

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