whop.ucsc.genesForRegion: Return a list of genes located in a certain region on a...

In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description

Details on all genes falling into the positions between 'beg' and 'end' on chromosome 'chrom' are returned.

Usage

whop.ucsc.genesForRegion(chrom, beg, end)

Arguments

chrom	Chromosome on which to look in "chr1" notation
beg	First position of the region a gene may fall into
end	Last position of the region a gene may fall into

Details

Gene name, chromosome of origin, strand, and start and end positions of transcription site, coding sequence and exons are returned.

Value

geneName	Gene name
name	Gene identifier
chrom	Chromosome, on which the gene is located
strand	Whether this gene is located on the + or - strand
txStart	Transcription start site
txEnd	Transcription end
cdsStart	Coding sequence start
cdsEnd	coding sequence end
exonCount	Number of exons of this gene
exonStarts	comma-separated list of exon start position
exonEnds	comma-separated list of exon end positions

Author(s)

Ulrich Wittelsbuerger

WhopGenome documentation built on May 1, 2019, 10:12 p.m.