distinct: Finds unique genes under peaks.

Description Usage Arguments Details Value Examples

Description

Determines what genes directly under peaks are actually unique between two different upstream extension levels.

Usage

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distinct(organism, start, end)

Arguments

organism

Object name assigned from readGFF() command.

start

Lower bound of upstream extension.

end

Upper bound of upstream extension.

Details

V1-V3 denote the chromosome/start/end positions of the peaks, V4-V6 denote the respective values of the genes, V7 is the gene ID (e.g., Ensembl ID), V8 is the gene name, and V9 is the distance of peak to nearest gene.

Value

A data.table of unique genes located under peaks between two upstream extension levels.

Examples

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library(rtracklayer)
rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
peaksInput(fpath)
distinct(rat, 2000, 3000)

Bohdan-Khomtchouk/geneXtendeR_keepme documentation built on June 3, 2019, 10:09 p.m.