Functionality related to DNA/RNA sequences

Description

Utility functions related to RNA/DNA sequences, such as extracting RNA/DNA sequences for features defined in Ensb.

Usage

## S4 method for signature 'EnsDb'
getGenomeFaFile(x, pattern="dna.toplevel.fa")

Arguments

(In alphabetic order)

Value

For getGenomeFaFile: a FaFile-class object with the genomic DNA sequence.

Methods and Functions

getGenomeFaFile

Returns a FaFile-class (defined in Rsamtools) with the genomic sequence of the genome build matching the Ensembl version of the EnsDb object. The file is retrieved using the AnnotationHub package, thus, at least for the first invocation, an internet connection is required to locate and download the file; subsequent calls will load the cached file instead. If no fasta file for the actual Ensembl version is available the function tries to identify a file matchint the species and genome build version of the closest Ensembl release and returns that instead. See the vignette for an example to work with such files.

Author(s)

Johannes Rainer

See Also

BasicFilter transcripts exonsBy

Examples

## Loading an EnsDb for Ensembl version 75 (genome GRCh37):
library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75

## Not run: 
    ## Retrieve a FaFile with the gneomic DNA sequence matching the organism,
    ## genome release version and, if possible, the Ensembl version of the
    ## EnsDb object.
    Dna <- getGenomeFaFile(edb)
    ## Extract the transcript sequence for all transcripts encoded on chromosome
    ## Y.
    ##extractTranscriptSeqs(Dna, edb, filter=SeqnameFilter("Y"))


## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ensembldb)
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: GenomicRanges
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: GenomicFeatures
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/ensembldb/EnsDb-sequences.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getGenomeFaFile
> ### Title: Functionality related to DNA/RNA sequences
> ### Aliases: getGenomeFaFile getGenomeFaFile,EnsDb-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> ## Loading an EnsDb for Ensembl version 75 (genome GRCh37):
> library(EnsDb.Hsapiens.v75)
> edb <- EnsDb.Hsapiens.v75
> 
> ## Not run: 
> ##D     ## Retrieve a FaFile with the gneomic DNA sequence matching the organism,
> ##D     ## genome release version and, if possible, the Ensembl version of the
> ##D     ## EnsDb object.
> ##D     Dna <- getGenomeFaFile(edb)
> ##D     ## Extract the transcript sequence for all transcripts encoded on chromosome
> ##D     ## Y.
> ##D     ##extractTranscriptSeqs(Dna, edb, filter=SeqnameFilter("Y"))
> ##D 
> ## End(Not run)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>