collapse.gct2geneset: Collapse a GCT file from 1 row per gene to 1 row per geneset.

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

Description

This function collapses gene data to geneset data. NB: the gct[,1] must be the same as the ID's in the gmt file. Usually, GCT files have probe names in column 1, and GMT files have gene symbols. Thus you need to collapse the GCT file to 1 row per gene symbol (see collapse.gct). Currently supported methods include: mean, median which are good if you expect all genes in the pathway to be similarly changed min, max if you're looking at pathways with high or low abundance sum which is good if the gct file is an adjacency matrix (eg summing up the number of genes that are mutated in a pathway)

Usage

collapse.gct2geneset(gct.file, gmt.file, method = c("mean", "median", "min",
  "max", "sum"), min.size = 1, max.size = 1e+05, gct.out = NULL)

Arguments

gct.file	the path to a gct file
gmt.file	the path to a gmt file. untested with a gmx file
method	one of mean, median, min, max, sum
min.size	minimum size threshold for each geneset. default=1, ie include all genesets with >= 1 gene. GSEA default = 15
max.size	maximum size threshold for each geneset. default=1e05, ie include all genesets. GSEA default = 500
gct.out	the path to the output gct file. This will overwrite any previous file there.

Value

side effect of creating a file at gct.out, with 1 row per geneset, as long as the geneset passed the size thresholds. Todo: add PGSEA, maxmean, maxvar as an option See also: collapse.gct

Author(s)

Mark Cowley, 2011-02-27

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