gene_from_regions: Given a set of regions, convert it to a set of Entrez gene...

Description Usage Arguments Value

View source: R/AnnotationHelper.R

Description

Utility function to get a gene list from a set of regions.

Usage

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gene_from_regions(regions, annotations.list, flank.size = c(-3000, 3000),
  region.types = c("Gene body", "Promoter", "Downstream", "Distal", "All"))

Arguments

regions

A GRanges object with regions to be associated to genes.

annotations.list

A list of annotation databases returned by select_annotations.

flank.size

The extent around the TSS which is considered the promoter region.

region.types

A character vector representing region types which will cause a gene association. These can be:

Promoter

Promoter region (upstream and downstream of the TSS).

Gene body

Promoter, Exons, introns, 5' and 3' UTRs.

Downstream

Region downstream of the TES.

Distal

Regions which do not fit any of the above category.

All

All of the above.

Value

A data-frame with the enrichment results.


ArnaudDroitLab/ef.utils documentation built on June 19, 2018, 8:26 p.m.