GappedReads-class

(Legacy) GappedReads objects

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.

Keywords
classes, methods
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 a DNAStringSet object.

References

http://samtools.sourceforge.net/

See Also

Aliases
  • class:GappedReads
  • GappedReads-class
  • GappedReads
  • qseq
  • qseq,GappedReads-method
  • qwidth,GappedReads-method
  • c,GappedReads-method
Examples
greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
greads <- readGappedReads(greads_file)
greads
qseq(greads)
Documentation reproduced from package GenomicAlignments, version 1.2.2, License: Artistic-2.0

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