proteinCoding

proteinCoding-methods

proteinCoding,GRanges-method

proteinCoding,GRangesList-method

Removed all the ranges that are not protein coding. Typically used on
 the output of <code><a rd-options="" href="/link/etrid2grl?package=Pbase&version=0.12.2" data-mini-rdoc="Pbase::etrid2grl">etrid2grl</a></code> before
 <code><a rd-options="" href="/link/mapToGenome?package=Pbase&version=0.12.2" data-mini-rdoc="Pbase::mapToGenome">mapToGenome</a></code>.

methods

A set of classes and functions to investigate and
understand protein sequence data in the context of a
proteomics experiment.

Laurent Gatto

Pbase

Manipulating and exploring protein and proteomics data

proteinCoding-methods function

<dl> <dt><code>signature(object="GRanges", mcol="character",
	coding="character")</code></dt><dd> Removes all the ranges that are not
	annotated as protein coding ranges, i.e. ranges whose
	<code>mcols()$mcol</code> is different from <code>coding</code>. The default
	values are <code>mcols()feature</code> and
	<code>"protein_coding"</code>. The method return the <code>GRanges</code>
	trimmed from all non-matching ranges.
 </dd> <dt><code>signature(object="GRangesList", mcol="character",
	coding="character")</code></dt><dd>As above but for <code>GRanges</code> in a
 <code>GrangesList</code>.
 </dd> </dl>

Methods

Removed all the ranges that are not protein coding. Typically used on
 the output of <code><a href="etrid2grl" rd-options="">etrid2grl</a></code> before
 <code><a href="mapToGenome" rd-options="">mapToGenome</a></code>.

proteinCoding-methods: Only keep protein coding ranges

Description

Arguments

Methods