locusdef.rn4.1kb_outside: locusdef.rn4.1kb_outside locus definition

Description Usage Format Details Source

Description

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

Usage

1

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.


wangk4/chipenrich.data documentation built on June 19, 2020, 12:18 a.m.