importGeneSets: Import gene sets stored in GMT, GMX, GRP, and XML file formats
Description
Imports gene sets stored in GMT, GMX, GRP, and XML file formats and
converts them to sigPathway's preferred format.
Usage
importGeneSets(fileNames, verbose = TRUE)
gmtToG(fileNames, verbose = TRUE)
gmxToG(fileNames, verbose = TRUE)
grpToG(fileNames, verbose = TRUE)
xmlToG(fileNames, verbose = TRUE)
Arguments
fileNames
a character vector specifying the file(s) containing the gene
sets of interest
verbose
a boolean to indicate whether to print debugging messages
to the R console
Value
A list containing sublists representing each imported gene set. The
vignette contains more details about the list structure.
Details
These functions read in gene sets stored in GMT, GMX, GRP, and XML
file formats and converts them to a list format that sigPathway can
use. Redundant gene IDs in each gene set are removed during
conversion. The importGeneSets function can read in GMT, GMX,
GRP, and XML files in one pass. The gmtToG, gmxToG,
grpToG, and xmlToG functions are specific to reading in
their respective file formats.