kegg_enrichment: Perform KEGG pathway enrichment on a set of genes.

Description Usage Arguments Value

View source: R/AnnotationHelper.R

Description

Utility function which performs the same operations as motif_enrichment, but accepts a list of genes instead of a list of regions.

Usage

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kegg_enrichment(selected.genes, annotations.list, filename = NULL,
  diseases = FALSE, gene.background = NULL)

Arguments

selected.genes

A vector of ENTREZ gene ids to be subjected to motif enrichment.

annotations.list

A list of annotation databases returned by select_annotations.

filename

The name of the file where the results should be saved. If NULL, results are not saved to disk.

diseases

If TRUE, the enrichment is performed against the disease pathways.

gene.background

A list of Entrez gene ids of the genes to be used as the background of the enrichment. If NULL, all genes in annotations.list$TxDb are used.

Value

A data-frame with the enrichment results.


ArnaudDroitLab/ef.utils documentation built on Aug. 13, 2019, 9:09 p.m.