load_gmt_signatures: Load signatures from either a gmt file, xml file, or directly...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Load signatures from either a gmt file, xml file, or directly from the GSVAdata data set in R.

Description

There are a bunch of places from which to acquire signature data. This function attempts to provide a single place to load them. The easiest way to get up to date signatures is to download them from msigdb and set the signatures parameter to the downloaded filename.

Usage

load_gmt_signatures(
  signatures = "c2BroadSets",
  data_pkg = "GSVAdata",
  signature_category = "c2",
  id_type = "entrez"
)

Arguments

signatures	Either the filename downloaded or the variable's name as found in the environment created by data_pkg.
data_pkg	Used when signatures is not a filename to load a data package, presumably GSVAdata.
signature_category	Probably not needed unless you download a signature file containing lots of different categories.
id_type	Specify the ID type in the data.

Value

signature dataset which may be used by gsva()

See Also

[GSEABase]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.