runKEGG.all: Run KEGG analysis on a multi-sample results table.

In sansomlab/gsfisher: Geneset Fisher

Run KEGG analysis on a multi-sample results table.

Description

Run KEGG analysis on a multi-sample results table.

Usage

runKEGG.all(
  results = NULL,
  species = c("mm", "hs"),
  background_ids = NULL,
  sample_col = "cluster",
  gene_id_col = "gene_id",
  gene_id_type = c("entrez", "ensembl"),
  keggData = 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".
keggData	A list of KEGG gene sets. (see fetchKegg).
p_col	The column containing the p-values to use
p_threshold	The significance threshold.

sansomlab/gsfisher documentation built on July 7, 2022, 4:21 a.m.