Convert a supported reference sequence argument to a DNAStringSet — refargToDNAStringSet • SingleMoleculeGenomicsIO

This function takes a supported argument value specifying the reference sequence (e.g. genome) and returns it as a DNAStringSet object. Currently supported argument values are:

"BSgenome:": : A BSgenome object
"DNAStringSet": : A DNAStringSet object
"character": : A path to a fasta file

Usage

refargToDNAStringSet(sequenceReference)

Arguments

sequenceReference: A supported value defining the reference sequence.

Value

A DNAStringSet object.

Author

Michael Stadler, Charlotte Soneson

Examples

ref <- refargToDNAStringSet(system.file("extdata", "reference.fa.gz",
                                        package = "SingleMoleculeGenomicsIO"))
ref
#> DNAStringSet object of length 1:
#>       width seq                                             names               
#> [1] 6957060 NNNNNNNNNNNNNNNNNNNNNN...GACAGTAATCCAGGAAAGGGGA chr1