derep-class


A <code><a rd-options="" href="/link/list?package=dada2&version=1.0.3" data-mini-rdoc="dada2::list">list</a></code> with the following three members.
<ul>
<li>$uniques: Named integer vector. Named by the unique sequence, valued by abundance.
 </li>
<li>$quals: Numeric matrix of average quality scores by position for each unique. Uniques are rows, positions are cols.
 </li>
<li>$map: Integer vector of length the number of reads, and value the index (in $uniques) of the unique to which that read was assigned.
</li>
</ul><p></p><p>This can be created from a FastQ sequence file using
<code><a rd-options="" href="/link/derepFastq?package=dada2&version=1.0.3" data-mini-rdoc="dada2::derepFastq">derepFastq</a></code>
</p>

The dada2 package provides "OTU picking" functionality, but instead
of picking OTUs the DADA2 algorithm exactly infers samples sequences. The dada2
pipeline starts from demultiplexed fastq files, and outputs inferred sample
sequences and associated abundances after removing substitution and chimeric
errors. Taxonomic classification is also available via a native implementation
of the RDP classifier method.

Benjamin Callahan

dada2

Accurate, high-resolution sample inference from amplicon
sequencing data

derep-class function

A <code><a href="list" rd-options="">list</a></code> with the following three members.
<ul><li>$uniques: Named integer vector. Named by the unique sequence, valued by abundance.</li></ul>
 <item>$quals: Numeric matrix of average quality scores by position for each unique. Uniques are rows, positions are cols.</item>
 <item>$map: Integer vector of length the number of reads, and value the index (in $uniques) of the unique to which that read was assigned.</item>

derep-class: A class representing dereplicated sequences

Description

Arguments

See Also