Gene set enrichment analysis (GSEA) from a VISTA comparison

Usage

get_gsea(
  x,
  sample_comparison,
  set_type = c("msigdb", "go", "kegg"),
  from_type = "SYMBOL",
  orgdb = NULL,
  species = "Mus musculus",
  msigdb_category = "H",
  msigdb_subcategory = NULL,
  ...
)

Arguments

x: A VISTA object with DE results.
sample_comparison: Comparison name to use.
set_type: One of "msigdb", "go", or "kegg" selecting the gene set source.
from_type: Identifier type in the DE tables (default "SYMBOL").
orgdb: OrgDb object; defaults to mouse/human based on species.
species: Species name to infer default OrgDb.
msigdb_category, msigdb_subcategory: Passed to msigdbr::msigdbr() when set_type = "msigdb".
...: Additional arguments forwarded to the underlying GSEA function: clusterProfiler::GSEA() (msigdb TERM2GENE), gseGO(), or gseKEGG() depending on set_type.

Value

An object returned by this function.

Examples

if (FALSE) { # \dontrun{
v <- example_vista()
comp <- names(comparisons(v))[1]
if (requireNamespace('msigdbr', quietly = TRUE)) {
  out <- try(get_gsea(v, sample_comparison = comp, set_type = 'msigdb', from_type = 'ENSEMBL', species = 'Homo sapiens'), silent = TRUE)
  if (!inherits(out, 'try-error')) out
}
} # }