motif_enrichment_genes: Perform motif enrichment on the promoters of a set of genes.

In ArnaudDroitLab/ef.utils: Eric Utilities

Description

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

Usage

motif_enrichment_genes(selected.genes, annotations.list, flank.size = 1000,
  ...)

Arguments

selected.genes	A vector of ENTREZ gene ids whose promoters should be subjected to motif enrichment.
annotations.list	A list of annotation databases returned by select_annotations.
flank.size	How many base pairs upstream of the TSS should we retrieve?
...	Additional arguments for motif_enrichment.

Value

A list with the following elements:

Region

The subset of regions where motifs were sought.

Enrichment

The result of the PWMEnrich motifEnrichment call.

Report

The result of the PWMEnrich groupReport call.

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