locusdef.rn4.1kb_outside_upstream: locusdef.rn4.1kb_outside_upstream locus definition

In sartorlab/chipenrich.data: Companion package to chipenrich

locusdef.rn4.1kb_outside_upstream locus definition

Description

A LocusDefinition where a gene locus is defined as the region beyond 1kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.

Usage

locusdef.rn4.1kb_outside_upstream

Format

A LocusDefinition object with the following slots:

granges

A GRanges of the locus definitions with mcols for Entrez Gene ID gene_id and gene symbol symbol

dframe

A data.frame of the locus definitions with columns for chr, start, end, gene_id, and symbol

genome.build

A character indicating the genome build. In this case, rn4.

organism

A character indicating the organism name. In this case, Rattus norvegicus.

Details

For the rn4 genome, original gene IDs are from ENSEMBL and so an additional step of converting to Entrez IDs is done.

Built on Fri Apr 13 09:52:01 2018.

Source

R packages: TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 and org.Rn.eg.db_3.5.0.

sartorlab/chipenrich.data documentation built on Oct. 4, 2023, 5:21 p.m.