| GappedReads-class {GenomicAlignments} | R Documentation |
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.
GappedReads objects are typically created when reading a file
containing aligned reads with the readGappedReads
function.
In the code snippets below, x is a GappedReads object.
qseq(x):
Extracts the sequences of the queries as a
DNAStringSet object.
Hervé Pagès
http://samtools.sourceforge.net/
GAlignments objects.
greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
greads <- readGappedReads(greads_file)
greads
qseq(greads)