readGMT: Import Gene Sets from a GMT File

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

Import Gene Sets from a GMT File

Description

Imports a list of gene sets from a GMT (Gene Matrix Transposed) format file, offering a choice of ways to handle duplicated gene set names.

Usage

readGMT(
  con,
  deduplUse = c("first", "drop", "union", "smallest", "largest", "custom")
)

Arguments

con

A connection object or character string containing e.g. a file name or URL. This is directly passed to readLines and hence may contain anything that readLines() can handle.

deduplUse

With the exception of the special method custom, all handling of duplicated gene set names is delegated to function deduplicateGeneSets and this argument is directly passed on. Please see ?deduplicateGeneSets. Using deduplUse=custom allows import of the GMT file for manual inspection and its content and remedy is the user's responsibility. However, gsva() will not accept the result for further use unless it is modified to have duplicated gene set names removed.

Value

A named list of gene sets that represented as character vectors of gene IDs.

See Also

readLines, deduplicateGeneSets

rcastelo/GSVA documentation built on May 9, 2024, 7:23 p.m.