Perform MSigDB over-representation analysis on a VISTA object

This function performs ORA on a set of genes from a VISTA object. Gene identifiers stored as “ENSG00000187634:SAMD11” will be split at the colon and the appropriate part extracted based on from_type. Genes are then optionally converted via orgdb to match the identifier type required by the MSigDB gene sets.

Usage

enrichMsigDB(
  x,
  gene_list,
  from_type = "SYMBOL",
  orgdb,
  msigdb_category = "H",
  msigdb_subcategory = NULL,
  species = "Mus musculus",
  background = NULL,
  col_genetype = "GENETYPE",
  feature_type = "protein-coding",
  ...
)

Arguments

x: A VISTA object.
gene_list: A non-empty character vector of gene identifiers. This argument is required and must not be NULL.
from_type: Identifier type of the genes in gene_list. One of "SYMBOL", "ENSEMBL", or "ENTREZID" (default "SYMBOL"). Ensembl IDs have version suffixes stripped automatically.
orgdb: An OrgDb object used for ID conversion. If omitted, a default is chosen based on species: org.Mm.eg.db for mouse, org.Hs.eg.db for human.
msigdb_category: MSigDB category (e.g. "H", "C2", "C5"). Default "H".
msigdb_subcategory: Optional MSigDB sub-collection (e.g. "BP" for C5). Default NULL.
species: Species name for MSigDB (default "Mus musculus").
background: Optional character vector of background gene IDs. If NULL, all features in the VISTA object (optionally filtered by feature_type) are used.
col_genetype: Column name in rowData(x) used to filter the background by gene type (default "GENETYPE").
feature_type: Gene type to retain in the background when background is NULL (default "protein-coding").
...: Additional arguments to pass to clusterProfiler::enricher().

Value

A list containing a single enrichResult object named "enrich".