geneSetAnalysis: Perform a gene set analysis on a gene

In EvgeniyaGorobets/PGxVision: Visualize Biomarkers and Pharmacogenomic Data

Description

Query MSigDb to find all gene sets that query gene is in, then compute the similarity of the gene sets. Return both the similarity scores and the gene set information that was retrieved. This is a wrapper function which performs the full gene set analysis pipeline (not including buildNetworkPlot). Note that this function is computationally heavy and may take a while to run (this is mostly due to large, slow MSigDb API queries).

Usage

geneSetAnalysis(geneId, queryType, similarityMetric = "overlap")

Arguments

geneId	The ENSEMBL ID of the gene you want to query
queryType	The type of gene sets you want to retrieve; see MSigDb for possible subcategories (use msigdbr::msigdbr_collections())
similarityMetric	The algorithm used to compute the similarity between gene sets. The default (and only option currently) is "overlap".

Value

A named list with two fields: "geneSets" and "similarityDf". "geneSets" contains a data.table of all the gene sets containing the query gene and belonging to the queryType category (see ?PGxVision::getGeneSets for more info). "similarityDf" contains a data.frame with the similarity scores for each pair of gene sets (see ?PGxVision::computeGeneSetSimilarity for more info).

Examples

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

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