motif_enrichment: Given a GRanges object, finds enriched motifs within those...

In ArnaudDroitLab/ef.utils: Eric Utilities

Description

Performs motif enrichment against pwm.bg. If pwm.bg is not provided, annotations.list$PWMBG is used.

Usage

motif_enrichment(regions, annotations.list, file.label = NULL,
  pwm.bg = NULL, top.x = 20)

Arguments

regions	The regions on which motif enrichment should be performed.
annotations.list	A list of annotation databases returned by select_annotations.
file.label	A label for generating file names to save the results. If NULL, results are not saved to disk.
pwm.bg	A PWMLogn background object against which enrichment should be performed.
top.x	Number of top motifs for which logos are generated.

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.