preparePromoterAnnotation {proActiv} | R Documentation

## Prepares promoter annotation from a gtf or txdb

### 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')

[Package proActiv version 1.2.0 Index]