getGeneSets: Get gene set info based on a query gene

In EvgeniyaGorobets/PGxVision: Visualize Biomarkers and Pharmacogenomic Data

Description

Get all gene sets from MSigDb that contain the query gene and belong to the queryType category. Examples of gene set categories are biological processes, cellular components, pathways, molecular functions, etc. Return information about all retrieved gene sets.

Usage

getGeneSets(geneId, queryType)

Arguments

geneId	The ENSEMBL ID of the gene you want to query
queryType	The type of query you want to perform, i.e., the category of the gene sets you are retrieving. See MSigDb for possible subcategories (use msigdbr::msigdbr_collections())

Value

A data.table containing all the gene sets in the category queryType and containing the query gene. The data.table contains gene set ID (gs_id), name (gs_name), source (gs_exact_source), URL (gs_url), and description (gs_description).

Examples

getGeneSets("ENSG00000000971", "GO:BP")

EvgeniyaGorobets/PGxVision documentation built on Dec. 17, 2021, 7:26 p.m.