ampliconfreqs.long


A data frame with 16 amplicon data sets taken from 8 different sampling sites. 
Samples from each sampling site were sequenced twice, corresponding to sets A and B (e.g. column  FU25.A and FU25.B). 
Names of the sampling sites are specified in the data <code><a rd-options="" href="/link/site.f?package=AmpliconDuo&version=1.1" data-mini-rdoc="AmpliconDuo::site.f">site.f</a></code>.


datasets

Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.

Anja Lange

AmpliconDuo

Statistical Analysis of Amplicon Data of the Same Sample to
Identify Artefacts

ampliconfreqs.long function

A data frame with 80903 observations on the following 16 variables.
  <dl>
    <dt><code>FU25.A</code></dt><dd>a numeric vector</dd> <dt><code>FU25.B</code></dt><dd>a numeric vector</dd> <dt><code>FU28.A</code></dt><dd>a numeric vector</dd> <dt><code>FU28.B</code></dt><dd>a numeric vector</dd> <dt><code>FU31.A</code></dt><dd>a numeric vector</dd> <dt><code>FU31.B</code></dt><dd>a numeric vector</dd> <dt><code>FU31.C</code></dt><dd>a numeric vector</dd> <dt><code>FU31.D</code></dt><dd>a numeric vector</dd> <dt><code>FU34.A</code></dt><dd>a numeric vector</dd> <dt><code>FU34.B</code></dt><dd>a numeric vector</dd> <dt><code>FU37.A</code></dt><dd>a numeric vector</dd> <dt><code>FU37.B</code></dt><dd>a numeric vector</dd> <dt><code>UniPond.A</code></dt><dd>a numeric vector</dd> <dt><code>UniPond.B</code></dt><dd>a numeric vector</dd> <dt><code>BogSoil.A</code></dt><dd>a numeric vector</dd> <dt><code>BogSoil.B</code></dt><dd>a numeric vector</dd> </dl> 

ampliconfreqs.long: SSU Amplicon Frequencies Of Different Sampling Sites

Description

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