runGMT.all: Run GMT analysis on a multi-sample results table.
In sansomlab/gsfisher: Geneset Fisher

runGMT.all

R Documentation

Run GMT analysis on a multi-sample results table.

Description

Run GMT analysis on a multi-sample results table.

Usage

runGMT.all(
  results = NULL,
  species = c("mm", "hs"),
  background_ids = NULL,
  sample_col = "cluster",
  gene_id_col = "gene_id",
  gene_id_type = c("entrez", "ensembl"),
  gmt_file = NULL,
  p_col = "p_val_adj",
  p_threshold = 0.1
)

Arguments

`results`	A multi-sample results table
`species`	Either "mm" or "hs"
`background_ids`	A vector of ENSEMBL gene ids. If NULL, taken from results.
`sample_col`	The column in results that indicates the sample
`gene_id_col`	The column containing the gene identifiers
`gene_id_type`	Either "entrez" (default) or "ensembl".
`gmt_file`	A GMT file.
`p_col`	The column containing the p-values to use
`p_threshold`	The significance threshold.