importGeneSets {sigPathway}R Documentation

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

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.

Value

A list containing sublists representing each imported gene set. The vignette contains more details about the list structure.

Note

These functions do not check whether the files are in the correct format and will give spurious output when given files in the wrong format. The 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.

Author(s)

Weil Lai

References

http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats


[Package sigPathway version 1.10.0 Index]