promoterRegions: Generate annotation for promoter region of genes

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/promoterRegions.R

Description

Create a SAF data.frame of genewise promoter regions

Usage

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promoterRegions(annotation="mm10", upstream=3000L, downstream=2000L)

Arguments

annotation

a character string giving the name of a genome with built-in annotation or a SAF format gene annotation. If using built-in annotation, the character string should be one of the following: mm10, mm9, hg38 or hg19. They correspond to the NCBI RefSeq annotations for genomes ‘mm10’, ‘mm9’, ‘hg38’ and ‘hg19’, respectively. mm10 by default.

upstream

an integer giving the number of upstream bases that will be inclued in the promoter region generated for each gene. These bases are taken immediately upstream (5' end) from transcriptional start site of each gene.

downstream

an integer giving the number of downstream bases that will be inclued in the promoter region generated for each gene. These bases are taken immediately downstream (3' end) from transcriptional start site of each gene.

Details

This function takes as input a SAF format gene annotation and produces a SAF format annotation that contains chromosomal coordinates of promoter region of each gene. See featureCounts for definition of the SAF format.

Built-in annotations can be accessed via function getInBuiltAnnotation.

Value

A SAF format data.frame with columns GeneID, Chr, Start, End and Strand.

Author(s)

Gordon K Smyth

See Also

featureCounts, getInBuiltAnnotation

Examples

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library(Rsubread)
x <- promoterRegions()
head(x)

Example output

NCBI RefSeq annotation for mm10 (build 38.1).
      GeneID  Chr   Start     End Strand
4  100503874 chr1 3656904 3661904      -
1     497097 chr1 3669498 3674498      -
6  100038431 chr1 3677155 3681788      +
7      19888 chr1 4407241 4412241      -
13     20671 chr1 4494413 4499413      -
18     27395 chr1 4783726 4788726      -

Rsubread documentation built on Nov. 9, 2018, 6 p.m.