prep.msigdb {GSDA}

Preparation of MSigDB for 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)