locusdef.hg19.5kb_outside_upstream: locusdef.hg19.5kb_outside_upstream locus definition

In sartorlab/chipenrich.data: Companion package to chipenrich

locusdef.hg19.5kb_outside_upstream locus definition

Description

A LocusDefinition where a gene locus is defined as the region beyond 5kb upstream of the TSS and bounded by the midpoint between the TSS and the next upstream TSS.

Usage

locusdef.hg19.5kb_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, hg19.

organism

A character indicating the organism name. In this case, Homo sapiens.

Details

Built on Fri Apr 13 09:45:57 2018.

Source

R packages: TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 and org.Hs.eg.db_3.5.0. GENCODE resources: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz and ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.metadata.EntrezGene.gz

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