getGenomeFaFile {ensembldb} | R Documentation

## 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")

    ## S4 method for signature 'EnsDb'
    getGenomeTwoBitFile(x)

### Arguments

(In alphabetic order)

`pattern` | For method `getGenomeFaFile`: the pattern to be used to identify the fasta file representing genomic DNA sequence.
`x` | An `EnsDb` instance.

### Value

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

For `getGenomeTwoBitFile`: a `TwoBitFile-class` object with the genome 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 matching 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.

getGenomeTwoBitFile

  Returns a `TwoBitFile-class` (defined in the `rtracklayer` package) with the genomeic sequence of the genome build matching the Ensembl version of the `EnsDb` object. The file is retrieved from `AnnotationHub` and hence requires (at least for the first query) an active internet connection to download the respective resource. If no DNA sequence matching the Ensembl version of `x` is available, the function tries to find the genomic sequence of the best matching genome build (closest Ensembl release) and returns that.

  See the `ensembldb` vignette for details.

### Author(s)

Johannes Rainer

### See Also

`transcripts` `exonsBy`

### Examples

    ## Loading an EnsDb for Ensembl version 86 (genome GRCh38):
    library(EnsDb.Hsapiens.v86)
    edb <- EnsDb.Hsapiens.v86

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

    ## End(Not run)

[Package ensembldb version 2.16.4 Index]