class:GappedReads

GappedReads-class

GappedReads

qseq

qseq,GappedReads-method

qwidth,GappedReads-method

c,GappedReads-method


  The GappedReads class extends the <a rd-options="" href="/link/GAlignments?package=GenomicAlignments&version=1.8.4" data-mini-rdoc="GenomicAlignments::GAlignments">GAlignments</a> class.<p></p><p>  A GappedReads object contains all the information contained in a
  <a rd-options="" href="/link/GAlignments?package=GenomicAlignments&version=1.8.4" data-mini-rdoc="GenomicAlignments::GAlignments">GAlignments</a> object plus the sequences of the queries.
  Those sequences can be accessed via the <code>qseq</code> accessor.
</p>

classes

methods

Provides efficient containers for storing and manipulating
short genomic alignments (typically obtained by aligning short reads
to a reference genome). This includes read counting, computing the
coverage, junction detection, and working with the nucleotide content
of the alignments.

Bioconductor Package Maintainer

GenomicAlignments

Representation and manipulation of short genomic alignments

GappedReads-class function

GappedReads objects are typically created when reading a file
  containing aligned reads with the <code><a rd-options="" href="/link/readGappedReads?package=GenomicAlignments&version=1.8.4" data-mini-rdoc="GenomicAlignments::readGappedReads">readGappedReads</a></code>
  function.

Constructor

In the code snippets below, <code>x</code> is a GappedReads object. <dl>
    <dt></dt><dd>
      <code>qseq(x)</code>:
      Extracts the sequences of the queries as a
      <code><a rd-options="Biostrings" href="/link/DNAStringSet?package=GenomicAlignments&version=1.8.4&to=Biostrings" data-mini-rdoc="Biostrings::DNAStringSet">DNAStringSet</a></code> object.
    </dd> </dl> 

Accessors


  The GappedReads class extends the <a rd-options='' href='GAlignments'>GAlignments</a> class.

  A GappedReads object contains all the information contained in a
  <a rd-options='' href='GAlignments'>GAlignments</a> object plus the sequences of the queries.
  Those sequences can be accessed via the <code>qseq</code> accessor.


GappedReads objects are typically created when reading a file
  containing aligned reads with the <code><a rd-options='' href='readGappedReads'>readGappedReads</a></code>
  function.

GappedReads-class: (Legacy) GappedReads objects

Description

Arguments

Constructor

Accessors

References

See Also

Examples