getGMT: Import GMT (Gene Matrix Transposed) files

In llrs/BaseSet: Working with Sets the Tidy Way

Import GMT (Gene Matrix Transposed) files

Description

The GMT (Gene Matrix Transposed) file format is a tab delimited file format that describes groups of genes. In this format, each row represents a group. Each group is described by a name, a description, and the genes in it.

Usage

getGMT(con, sep = "\t", ...)

Arguments

con	File name of the GMT file.
sep	GMT file field separator, by default tabs.
...	Other arguments passed to readLines.

Value

A TidySet object.

References

The file format is defined by the Broad Institute here

See Also

Other IO functions: getGAF(), getOBO()

Examples

gmtFile <- system.file(
    package = "BaseSet", "extdata",
    "hallmark.gene.symbol.gmt"
)
gs <- getGMT(gmtFile)
nRelations(gs)
nElements(gs)
nSets(gs)

llrs/BaseSet documentation built on Feb. 22, 2025, 9:52 p.m.