GenomicFeatures (version 1.24.4)

getPromoterSeq: 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

"getPromoterSeq"(query, subject, upstream=2000, downstream=200, ...) "getPromoterSeq"(query, subject, upstream=2000, downstream=200, ...) "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

Value

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

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.

See Also

intra-range-methods ## promoters methods for Ranges objects intra-range-methods ## promoters methods for GRanges 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