import.gsea.chip: Import a GSEA chip file. This can look inside a gsea output...

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

Description

Missing values in chip files.
There seems to be little convention re missing values in chip files. It's important to map all potential missing values to NA's, since lots of code in this package assumes that the symbol is either valid, or NA. Set na.strings accordingly.

Usage

import.gsea.chip(x, na.strings = c("---", "NA", ""),
  capitalise.symbol = TRUE, verbose = FALSE)

Arguments

x	the path or url to a chip file, or the path to a gsea directory
na.strings	a character vector of values which should be mapped to NA. see details
capitalise.symbol	logical: capitalise all gene symbols upon import? see details
verbose	logical: if TRUE, then write out verbose messages, including download.file verbose output.

Details

Gene Symbol capitalisation.
GSEA likes to capitalise all gene symbols, so in GSEA result files, the symbols will be all caps. This can cause logical problems when using the symbol as a key. So, even though some human gene symbols are not supposed to be in caps, eg C1orf34, we recommend that you set capitalise.symbol=TRUE.

Author(s)

Mark Cowley, 2009-08-07

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