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

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 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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GenomicFeatures)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicFeatures/getPromoterSeq-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPromoterSeq
> ### Title: Get gene promoter sequences
> ### Aliases: getPromoterSeq getPromoterSeq,GRangesList-method
> ###   getPromoterSeq,GRanges-method
> ### Keywords: methods manip
> 
> ### ** Examples
> 
>   library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>   library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
>  
>   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
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>