distinct {geneXtendeR} | R Documentation

## Finds unique genes under peaks.

### 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

    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)

[Package geneXtendeR version 1.6.0 Index]