locusdef.mm9.1kb_outside: locusdef.mm9.1kb_outside locus definition

In sartorlab/chipenrich.data: Companion package to chipenrich

locusdef.mm9.1kb_outside locus definition

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

locusdef.mm9.1kb_outside

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, mm9.

organism

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

Details

Built on Fri Apr 13 09:50:42 2018.

Source

R packages: TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 and org.Mm.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.metadata.EntrezGene.gz

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