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<head><title>R: Utilities for manipulating chromosome and other 'seqname'
identifiers</title>
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<h1> Utilities for manipulating chromosome and other 'seqname'
identifiers
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</h1>
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</div><h2>Documentation for package ‘GenomeInfoDb’ version 1.6.0</h2>
<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
<li><a href="../doc/index.html">User guides, package vignettes and other documentation.</a></li>
<li><a href="../NEWS">Package NEWS</a>.</li>
</ul>
<h2>Help Pages</h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">as.data.frame-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="availableSpecies.html">available.species</a></td>
<td>Returns a data.frame that lists the available species strings and their taxonomy Ids.</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">bsgenomeName</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">bsgenomeName-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">class:GenomeDescription</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">class:Seqinfo</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">coerce-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">commonName</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">commonName-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="seqlevels-wrappers.html">dropSeqlevels</a></td>
<td>Convenience wrappers to the seqlevels() getter and setter</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">extractSeqlevels</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">extractSeqlevelsByGroup</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="fetchExtendedChromInfoFromUCSC.html">fetchExtendedChromInfoFromUCSC</a></td>
<td>Fetching chromosomes info for some of the UCSC genomes</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">genome</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">genome-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">genome-method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">genome<-</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">genome<--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">genome<--method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">GenomeDescription</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">GenomeDescription-class</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">genomeStyles</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">intersect-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">isCircular</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">isCircular-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">isCircular-method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">isCircular<-</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">isCircular<--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">isCircular<--method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqlevels-wrappers.html">keepSeqlevels</a></td>
<td>Convenience wrappers to the seqlevels() getter and setter</td></tr>
<tr><td style="width: 25%;"><a href="seqlevels-wrappers.html">keepStandardChromosomes</a></td>
<td>Convenience wrappers to the seqlevels() getter and setter</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">length-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">mapSeqlevels</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">merge-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">names-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">names<--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="rankSeqlevels.html">orderSeqlevels</a></td>
<td>Assign sequence IDs to sequence names</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">organism</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">organism-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">provider</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">provider-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">providerVersion</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">providerVersion-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="rankSeqlevels.html">rankSeqlevels</a></td>
<td>Assign sequence IDs to sequence names</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">releaseDate</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">releaseDate-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">releaseName</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">releaseName-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="seqlevels-wrappers.html">renameSeqlevels</a></td>
<td>Convenience wrappers to the seqlevels() getter and setter</td></tr>
<tr><td style="width: 25%;"><a href="seqlevels-wrappers.html">restoreSeqlevels</a></td>
<td>Convenience wrappers to the seqlevels() getter and setter</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">Seqinfo</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqinfo</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">Seqinfo-class</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">seqinfo-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqinfo<-</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlengths</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">seqlengths-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlengths-method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlengths<-</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">seqlengths<--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlengths<--method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevels</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">seqlevels-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevels-method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqlevels-wrappers.html">seqlevels-wrappers</a></td>
<td>Convenience wrappers to the seqlevels() getter and setter</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevels0</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevels<-</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">seqlevels<--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevels<--method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">seqlevelsInGroup</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevelsInUse</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqlevelsInUse-method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">seqlevelsStyle</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">seqlevelsStyle-method</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">seqlevelsStyle<-</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="seqlevelsStyle.html">seqlevelsStyle<--method</a></td>
<td>Conveniently rename the seqlevels of an object according to a given style</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqnames</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">seqnames-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">seqnames-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">seqnames<-</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">seqnames<--method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">show-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">show-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">sortSeqlevels</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="seqinfo.html">sortSeqlevels-method</a></td>
<td>Accessing/modifying sequence information</td></tr>
<tr><td style="width: 25%;"><a href="speciesMap.html">specData</a></td>
<td>Species Mapper object and/or list of valid taxonomy Ids</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">species</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="GenomeDescription-class.html">species-method</a></td>
<td>GenomeDescription objects</td></tr>
<tr><td style="width: 25%;"><a href="speciesMap.html">speciesMap</a></td>
<td>Species Mapper object and/or list of valid taxonomy Ids</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">summary-method</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">summary.Seqinfo</a></td>
<td>Seqinfo objects</td></tr>
<tr><td style="width: 25%;"><a href="speciesMap.html">validTaxIds</a></td>
<td>Species Mapper object and/or list of valid taxonomy Ids</td></tr>
<tr><td style="width: 25%;"><a href="Seqinfo-class.html">[-method</a></td>
<td>Seqinfo objects</td></tr>
</table>
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