Functionality related to DNA/RNA sequences
Utility functions related to RNA/DNA sequences, such as extracting
RNA/DNA sequences for features defined in Ensb.
## S4 method for signature 'EnsDb' getGenomeFaFile(x, pattern="dna.toplevel.fa") ## S4 method for signature 'EnsDb' getGenomeTwoBitFile(x)
(In alphabetic order)
pattern |
For method |
x |
An |
For getGenomeFaFile: a FaFile-class
object with the genomic DNA sequence.
For getGenomeTwoBitFile: a TwoBitFile-class
object with the genome sequence.
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.
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.
Johannes Rainer
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.