prep.msigdb: Preparation of MSigDB for GSDA

In GSDA: Gene Set Distance Analysis (GSDA)

Description

This function prepares the gene sets of a species in MsigDB for gene-set distance analysis.

Usage

prep.msigdb(species = "Homo sapiens", vset = "gs_name", vID = "gene_symbol")

Arguments

species	Name of species in MSigDB.
vset	Name of MSigDB column to use as vset in gsda, default is "gs_name".
vID	Name of MSigDB column to use as vID in gsda, default is "gene_symbol".

Details

Take a species from MsigDB (https://www.gsea-msigdb.org/gsea/msigdb/index.jsp), extract gene set definiton and prepare a data frame with gene sets and genes to be used as vset.data in the gsda function.

Value

A two-column data.frame with the columns vset and vID

Author(s)

Xueyuan Cao [e-mail] and Stanley Pounds [e-mail]

References

Cao X and Pounds S (2021) Gene-Set Distance Associations (GSDA): A Powerful Tool for Gene-Set Association Analysis.

Examples

gsets=prep.msigdb()
head(gsets)

GSDA documentation built on Jan. 18, 2021, 5:05 p.m.