ensembldb (version 1.4.6)

getGenomeFaFile: 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

## S3 method for class 'EnsDb':
getGenomeFaFile(x, pattern="dna.toplevel.fa")

Arguments

pattern

For method getGenomeFaFile: the pattern to be used to identify the fasta file representing genomic DNA sequence.

x

For all other methods an EnsDb instance.

Value

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

See Also

BasicFilter transcripts exonsBy

Examples

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

## 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"))