distinct: Finds unique genes under peaks.

In Bohdan-Khomtchouk/geneXtendeR_keepme: Optimized Functional Annotation Of ChIP-seq Data

Description

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

Usage

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

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.