BaseSet: getGMT – R documentation

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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", ...)

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

Examples

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

BaseSet

Working with Sets the Tidy Way

v0.0.16

MIT + file LICENSE

Authors

Lluís Revilla Sancho [aut, cre] (<https://orcid.org/0000-0001-9747-2570>), Zebulun Arendsee [rev], Jennifer Chang [rev]

Initial release