Fast Gene Set Enrichment Analysis — fgsea2 • MotrpacRatTraining6moWAT

Custom wrapper for fgsea for use with output of msigdbr2.

Usage

fgsea2(
  pathways,
  stats,
  gene_column = "entrez_gene",
  adjust.method = "BH",
  adjust.globally = TRUE,
  seed = NULL,
  ...
)

pathways: output of msigdbr2.
stats: output of rank_genes.
gene_column: character; the name of a column in pathways containing the genes in each pathway.
adjust.method: character; the p-value correction method. Can be abbreviated. See p.adjust.methods.
adjust.globally: logical; should p-values from all contrasts be adjusted together using adjust.method? Set to FALSE if the contrasts being tested are not closely related.
seed: numeric or NULL; passed to set.seed.
...: additional arguments passed to fgseaMultilevel.

A data.table with results for each contrast. See fgsea for more details.

Tyler Sagendorf