GappedReads-class {GenomicAlignments} | R Documentation |
(Legacy) GappedReads objects
Description
The GappedReads class extends the GAlignments class.
A GappedReads object contains all the information contained in a
GAlignments object plus the sequences of the queries.
Those sequences can be accessed via the qseq
accessor.
Constructor
GappedReads objects are typically created when reading a file
containing aligned reads with the readGappedReads
function.
Accessors
In the code snippets below, x
is a GappedReads object.
-
qseq(x)
: Extracts the sequences of the queries as aDNAStringSet
object.
Author(s)
Hervé Pagès
References
http://samtools.sourceforge.net/
See Also
-
GAlignments objects.
Examples
greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
greads <- readGappedReads(greads_file)
greads
qseq(greads)
[Package GenomicAlignments version 1.32.1 Index]