BaseSet (version 0.0.17)

getGMT: 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", ...)

Value

A TidySet object.

Arguments

con

File name of the GMT file.

sep

GMT file field separator, by default tabs.

...

Other arguments passed to readLines.

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)