getPromoterSeq {GenomicFeatures} | R Documentation

## Get gene promoter sequences

### Description

Extract sequences for the genes or transcripts specified in the query (aGRanges or GRangesList object) from a BSgenome object or an FaFile.

### Usage

      ## S4 method for signature 'GRangesList'
    getPromoterSeq(query, subject, upstream=2000, downstream=200, ...)
      ## S4 method for signature 'GRangesList'
    getPromoterSeq(query, subject, upstream=2000, downstream=200, ...)
      ## S4 method for signature 'GRanges'
    getPromoterSeq(query, subject, upstream=2000, downstream=200, ...)

### Arguments

`query` | A GRanges or GRangesList object containing genes grouped by transcript.
`subject` | A BSgenome object or a FaFile from which the sequences will be taken.
`upstream` | The number of DNA bases to include upstream of the TSS (transcription start site)
`downstream` | The number of DNA bases to include downstream of the TSS (transcription start site)
`...` | Additional arguments

### Details

`getPromoterSeq` is an overloaded method dispatching on query, which is either a GRanges or a GRangesList. It is a wrapper for the `promoters` and `getSeq` functions. The purpose is to allow sequence extraction from either a BSgenome or FaFile.

Default values for `upstream` and `downstream` were chosen based on our current understanding of gene regulation. On average, promoter regions in the mammalian genome are 5000 bp upstream and downstream of the transcription start site.

### Value

A DNAStringSet or DNAStringSetList instance corresponding to the GRanges or GRangesList supplied in the query.

### Author(s)

Paul Shannon

### See Also

intra-range-methods ## promoters method for IntegerRanges objects intra-range-methods ## promoters method for GenomicRanges objects getSeq

### Examples

      library(TxDb.Hsapiens.UCSC.hg19.knownGene)
      library(BSgenome.Hsapiens.UCSC.hg19)

      e2f3 <- "1871"  # entrez geneID for a cell cycle control transcription
                      # factor, chr6 on the plus strand

      transcriptCoordsByGene.GRangesList <-
         transcriptsBy (TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene") [e2f3]
        # a GrangesList of length one, describing three transcripts

      promoter.seqs <- getPromoterSeq (transcriptCoordsByGene.GRangesList,
                                       Hsapiens, upstream=10, downstream=0)
        # DNAStringSetList of length 1
        # [["1871"]] GCTTCCTGGA GCTTCCTGGA CGGAGCCAGG

[Package GenomicFeatures version 1.40.1 Index]