gbLocation-class

&#8220;gbLocation&#8221; is an S4 class that provides a container for
GenBank feature location descriptors.

classes

internal

Parse GenBank/GenPept records <https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html>
into native R objects to easily access and manipulate the sequence and annotation information.

Gerhard Schöfl

biofiles

An Interface for GenBank/GenPept Flat Files

gbLocation-class function

<dl class="dl-horizontal">
<dt><code>range</code></dt><dd>An integer matrix indicating the base numbers delimiting a
sequence span.</dd></dl><dt><code>fuzzy</code></dt><dd>A logical matrix indicating fuzzy start and/or end
(e.g. &lt;1..200).</dd><dt><code>strand</code></dt><dd>An integer vector containing -1, 1, or NA.</dd><dt><code>compound</code></dt><dd>A character code specifying how multiple ranges
are joined. One of &#8216;join&#8217;, &#8216;order&#8217;, or &#8216;bond&#8217;.</dd><dt><code>accession</code></dt><dd>A character vector; the accession number of the sequence
of the feature this location lives on.</dd><dt><code>remote</code></dt><dd>A logical vector</dd><dt><code>type</code></dt><dd>A character vector describing the type of the position. Normally
an "R" for &#8216;range&#8217; (e.g., <code>1..200</code> or point position <code>200</code>),
a "B" for &#8216;between bases&#8217; (e.g., <code>36^37</code>), or a "G" for gaps
(e.g., <code>gap()</code>, <code>gap(30)</code>, or <code>gap(unk30)</code>).</dd>

gbLocation-class: Class `"gbLocation"`

Description

Arguments

Slots

Details