importGeneSets: Import gene sets stored in GMT, GMX, GRP, and XML file...
In sigPathway: Pathway Analysis

Description Usage Arguments Details Value Note Author(s) References

Imports gene sets stored in GMT, GMX, GRP, and XML file formats and converts them to sigPathway's preferred format.

importGeneSets(fileNames, verbose = TRUE)
gmtToG(fileNames, verbose = TRUE)
gmxToG(fileNames, verbose = TRUE)
grpToG(fileNames, verbose = TRUE)
xmlToG(fileNames, verbose = TRUE)

`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

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.

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 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.

Weil Lai

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

sigPathway documentation built on Nov. 8, 2020, 5:35 p.m.