TwoBitFile-class {rtracklayer} | R Documentation |
The export.2bit
and import.2bit support the export and
import, respectively, of the UCSC 2bit compressed sequence format. The
main advantage is speed of subsequence retrieval, as it only loads the
sequence in the requested intervals. Compared to the FA format
supported by Rsamtools, 2bit offers the additional feature of masking
and also has better support in Java (and thus most genome
browsers). The supporting TwoBitFile
class is a reference to a
TwoBit file.
In the code snippets below, x
represents a TwoBitFile
object.
seqinfo(x)
:
Gets the Seqinfo
object
indicating the lengths of the sequences in the
file. No circularity or genome information is available.
import.2bit(con, which = as(seqinfo(con), "GenomicRanges"),
...)
: Imports sequence from 2bit file con
, which can be a
string (path or URL) or TwoBitFile
object. The sequence
retrieval is restricted to the intervals given by which
,
which should be something coercible to a GRanges
. The
returned DNAStringSet
contains a DNAString
for every
interval in which
.
export.2bit(object, con, which = as(seqinfo(con),
"GenomicRanges"), ...)
: Exports object
in the two bit
format to con
, a path or URL. The object
should be a
DNAStringSet
(or
something coercible to one) or a
BSgenome
object. If a
BSgenome
object, the arguments in ...
are passed
to bsapply
during the export
of each sequence.
Michael Lawrence
tbf <- TwoBitFile(system.file("tests", "test.2bit", package = "rtracklayer")) seqinfo(tbf) sequence <- import.2bit(tbf) # the whole file subrange <- IRanges::resize(as(seqinfo(tbf), "GenomicRanges"), width = 50) subsequence <- import.2bit(tbf, which = subrange)