Description Usage Arguments Value Author(s)
View source: R/gsea.gct.probes2genes.R
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".
1 2 | gsea.gct.probes2genes(data, stats, chip, mode = c("Best_probe", "Max_probe",
"Median_of_probes"))
|
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” |
a data.frame
of expression data with 1 row per unique gene symbol,
and gene symbols as the rownames see also gsea.genesets2gct
.
Mark Cowley, 2009-07-27
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