Imports gene sets stored in GMT, GMX, GRP, and XML file formats and converts them to sigPathway's preferred format.
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a character vector specifying the file(s) containing the gene sets of interest
a boolean to indicate whether to print debugging messages to the R console
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
importGeneSets function can read in GMT, GMX,
GRP, and XML files in one pass. The
xmlToG functions are specific to reading in
their respective file formats.
A list containing sublists representing each imported gene set. The vignette contains more details about the list structure.
These functions do not check whether the files are in the correct
format and will give spurious output when given files in the wrong
xmlToG function requires the
XML package, which
is available on CRAN. The
xmlToG function also requires XML
files to be formatted based on the MSigDB Document Type Definition.
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