readDefaultGenesets: Read default genesets for gene-set enrichment analysis

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Read default genesets for gene-set enrichment analysis

Description

In Roche Bioinformatics we use a default collection of gene-sets for gene-set enrichment analysis. This function loads this collection.

Usage

readDefaultGenesets(path, mps = FALSE)

Arguments

path	Character, path to the directory where the gmt files are stored
mps	Logical, whether molecular-phenotypic screening (MPS) genesets should be read in as pathway-centric namespaces (TRUE) or as one namespace named MolecularPhenotyping (FALSE).

Details

The default collection includes both publicly available genesets as well as proprietary genesets, and therefore they are not included as part of the ribios package.

Publicly available genesets include

• MSigDB: collections C2, C7 and Hallmark

• RONET: which is a collection of publicly available pathway databases including REACTOME and NCI-Nature

• goslim

Examples

## Not run: 
  ## this cannot be run because the files are not located there
  ## readDefaultGenesets("/tmp/defaultGmts")

## End(Not run)

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.