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 1.12.1 Index]