locusdef.mm10.nearest_gene: locusdef.mm10.nearest_gene locus definition

In sartorlab/chipenrich.data: Companion package to chipenrich

locusdef.mm10.nearest_gene locus definition

Description

A LocusDefinition where a gene locus is defined as the region spanning the midpoints between adjacent TSSs and TESs.

Usage

locusdef.mm10.nearest_gene

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, mm10.

organism

A character indicating the organism name. In this case, Mus musculus.

Details

Built on Fri Apr 13 09:51:33 2018.

Source

R packages: TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.metadata.EntrezGene.gz

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