MSigDBGeneSets: Create a list of gene sets for specific species from MSigDB...

Description Usage Arguments Value See Also Examples

View source: R/gsca_load_genesets.R

Description

This function creates gene set collections based on MSigDB database version 6.1. Currently our package only supports all 8 collections for Homo Sapiens as well as 'c2', 'c6' and 'c7' for Mus musculus. It returns a list of gene sets collections with the elements of the gene sets represented by Entrez Gene IDs.

Usage

1
MSigDBGeneSets(collection = "c2", species = "Hs")

Arguments

collection

A single character value specifying a choice of collection. Valid values include 'h'(hallmark gene sets), 'c1' (positional gene sets), 'c2' (curated gene sets), 'c3' (motif gene sets), 'c4' (computational gene sets), 'c5' (GO gene sets), 'c6' (oncogenic signatures), 'c7' (immunologic signatures). More details please refer to MSigDB.

species

A single character value specifying the species of the gene sets of MSigDB. Now we only support 'Hs' (Homo_Sapiens) for all 8 gene set collections and 'Mm' (Mus_musculus) for 'c2', 'c6' and 'c7' gene set collections.

Value

Return a list of gene sets of specific collection in MSigDB of version 6.1.

See Also

GOGeneSets, KeggGeneSets

Examples

1
C2_MSig <- MSigDBGeneSets(collection = "c2", species = "Hs")

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 11, 2018, 8:06 a.m.