Get gene promoter sequences
Extract sequences for the genes or transcripts specified in the query (aGRanges or GRangesList object) from a BSgenome object or an FaFile.
## 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, ...)
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 |
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.
A DNAStringSet or DNAStringSetList instance corresponding to the GRanges or GRangesList supplied in the query.
Paul Shannon
intra-range-methods ## promoters method for IntegerRanges objects intra-range-methods ## promoters method for GenomicRanges objects getSeq
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 CGGAGCCAGGPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.