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Import GMT (Gene Matrix Transposed) files

Source: R/GMT.R
getGMT.Rd

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)
#> [1] 7324
nElements(gs)
#> [1] 4386
nSets(gs)
#> [1] 50