locusdef.mm9.1kb_outside_upstream: locusdef.mm9.1kb_outside_upstream locus definition
In wangk4/chipenrich.data: Companion package to chipenrich
Description
Usage
Format
Details
Source
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
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, mm9.
- organism
A character indicating the organism name. In this case, Mus musculus.
Details
Built on Fri Apr 13 09:50:41 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
wangk4/chipenrich.data documentation built on June 19, 2020, 12:18 a.m.
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Description Usage Format Details Source
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
1 |
Format
A LocusDefinition object with the following slots:
- granges
A
GRangesof the locus definitions withmcolsfor Entrez Gene IDgene_idand gene symbolsymbol- dframe
A
data.frameof the locus definitions with columns forchr,start,end,gene_id, andsymbol- genome.build
A
characterindicating the genome build. In this case, mm9.- organism
A
characterindicating the organism name. In this case, Mus musculus.
Details
Built on Fri Apr 13 09:50:41 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
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