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

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Description

This function creates gene set collections based on MSigDB database version 6.2. Currently our package supports all 8 collections for 10 species retrieved by msigdbr. It returns a list of gene sets collections with the elements of the gene sets represented by Entrez Gene IDs.

Usage

MSigDBGeneSets(species = "Hs", collection = "C2", subcategory = NULL)

Arguments

species	A single character value specifying the species of the gene sets of MSigDB. Now we support 10 species: 'Bt'(Bos taurus), 'Ce'(Caenorhabditis elegans), 'Cfa'(Canis lupus familiaris), 'Dm'(Drosophila melanogaster), 'Dr'(Danio rerio), 'Gg'(Gallus gallus), 'Hs'(Homo sapiens), 'Mm'(Mus musculus), 'Rn'(Rattus norvegicus), 'Sc'(Saccharomyces cerevisiae) and 'Ss'(Sus scrofa).
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.

Value

Return a list of gene sets of specific collection in MSigDB of version 6.2.

See Also

GOGeneSets, KeggGeneSets

Examples

C2_MSig <- MSigDBGeneSets(species = "Hs", collection = "C2", subcategory = NULL)

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.