gbFeature-class

&#8220;gbFeature&#8221; is an S4 class that provides a container
for GenBank feature tables.

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

gbFeature-class function

<dl class="dl-horizontal">
<dt><code>.seqinfo</code></dt><dd>An <code><a href="/link/?package=biofiles&version=1.0.0" seqinfo'="" data-mini-rdoc="biofiles::"></a>'>seqinfo</code> object containing the
full-lenght sequence of the GenBank record that the feature is part
of as an <code><a href="/link/?package=biofiles&version=1.0.0" xstringset'="" data-mini-rdoc="biofiles::"></a>'>XStringSet</code> object, and sequence metadata
as a <code><a href="/link/?package=biofiles&version=1.0.0" gbheader'="" data-mini-rdoc="biofiles::"></a>'>gbHeader</code> object.</dd></dl><dt><code>.id</code></dt><dd>Identifier (index) of the feature in the GenBank record
the feature is part of.</dd><dt><code>key</code></dt><dd>The feature key.</dd><dt><code>location</code></dt><dd>A <code><a href="/link/?package=biofiles&version=1.0.0" gblocation'="" data-mini-rdoc="biofiles::"></a>'>gbLocation</code> object.</dd><dt><code>qualifiers</code></dt><dd>A named character vector. Name attributes
correspond to GenBank qualifier tags.</dd>

Slots

<code><a rd-options="" href="/link/getHeader?package=biofiles&version=1.0.0" data-mini-rdoc="biofiles::getHeader">getHeader</a></code>, <code><a rd-options="" href="/link/getSequence?package=biofiles&version=1.0.0" data-mini-rdoc="biofiles::getSequence">getSequence</a></code>,
<code><a rd-options="" href="/link/ranges?package=biofiles&version=1.0.0" data-mini-rdoc="biofiles::ranges">ranges</a></code>, <code><a rd-options="" href="/link/key?package=biofiles&version=1.0.0" data-mini-rdoc="biofiles::key">key</a></code>, <code><a rd-options="" href="/link/index?package=biofiles&version=1.0.0" data-mini-rdoc="biofiles::index">index</a></code>,
<code><a rd-options="" href="/link/qualif?package=biofiles&version=1.0.0" data-mini-rdoc="biofiles::qualif">qualif</a></code>

Accessor functions

Class <code>"gbFeature"</code> — gbFeature-class

<code><a rd-options='' href='getHeader'>getHeader</a></code>, <code><a rd-options='' href='getSequence'>getSequence</a></code>,
<code><a rd-options='' href='ranges'>ranges</a></code>, <code><a rd-options='' href='key'>key</a></code>, <code><a rd-options='' href='index'>index</a></code>,
<code><a rd-options='' href='qualif'>qualif</a></code>

gbFeature-class: Class `"gbFeature"`

Description

Arguments

Slots

Accessor functions

See Also