preparePromoterAnnotation: Prepares promoter annotation from a gtf or txdb

In proActiv: Estimate Promoter Activity from RNA-Seq data

Description

Prepares promoter annotation from a gtf or txdb

Usage

preparePromoterAnnotation(txdb, file, species)

Arguments

txdb	A txdb object. The txdb of the annotation version for which promoters will be identified. Either 'txdb' or 'file' argument must be specified, but not both.
file	A character object. The file path to a gtf/gff or txdb of the annotation version for which promoters will be identified. Either 'txdb' or 'file' argument must be specified, but not both.
species	A character object. The genus and species of the organism to be used in keepStandardChromosomes(). Supported species can be seen with names(genomeStyles()).

Value

A PromoterAnnotation object. The annotated intron ranges, promoter coordinates and the promoter id mapping are attributes of the promoter annotation data.

Examples

txdbPath <- system.file('extdata/vignette/annotations/',
                            'gencode.v34.annotation.subset.sqlite', 
                             package = 'proActiv')
txdb <- AnnotationDbi::loadDb(txdbPath)
promoterAnnotation <- preparePromoterAnnotation(txdb = txdb,
                                                species = 'Homo_sapiens')

proActiv documentation built on Nov. 8, 2020, 8:14 p.m.