AmpliconDuo: Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts
Version 1.1

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.

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AuthorAnja Lange [aut, cre], Daniel Hoffmann [aut]
Date of publication2016-01-19 13:09:23
MaintainerAnja Lange <anja.lange@uni-due.de>
LicenseGPL (>= 3)
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("AmpliconDuo")

Man pages

accepted.amplicons: List Of Amplicon Indices That Passed Filter Criteria
ampliconduo: Apply Fisher's Exact Tests To Two Amplicon Frequency Sets Of...
AmpliconDuo-package: Statistical Analysis Of Amplicon Data Of The Same Sample To...
ampliconfreqs: SSU Amplicon Frequencies Of Different Sampling Sites (Short...
ampliconfreqs.long: SSU Amplicon Frequencies Of Different Sampling Sites
amplicons: Example List of Ampliconduo Data Frames
discordance.delta: Measure Of Discordance Between Two Amplicon Data Sets
filter.ampliconduo: AmpliconDuo Amplicon Filter
filter.ampliconduo.set: AmpliconDuo List Amplicon Filter
plotAmpliconduo: Frequency-Frequency Plot Focusing On Significant Deviations...
plotAmpliconduo.set: Frequency-Frequency Plot Arrangement Focusing On Significant...
plotORdensity: Probability Density Plot Of Odds Ratios
site.f: Sampling Site Short Names

Functions

AmpliconDuo Man page
AmpliconDuo-package Man page
accepted.amplicons Man page Source code
ampliconduo Man page Source code
ampliconfreqs Man page
ampliconfreqs.long Man page
amplicons Man page
discordance.delta Man page Source code
filter.ampliconduo Man page Source code
filter.ampliconduo.set Man page Source code
plotAmpliconduo Man page Source code
plotAmpliconduo.set Man page Source code
plotORdensity Man page Source code
site.f Man page

Files

NAMESPACE
data
data/amplicons.rda
data/site.f.rda
data/ampliconfreqs.long.rda
data/ampliconfreqs.rda
R
R/ampliconduo.R
R/filter.ampliconduo.set.R
R/discordance.delta.R
R/filter.ampliconduo.R
R/plotAmpliconduo.set.R
R/plotAmpliconduo.R
R/accepted.amplicons.R
R/plotORdensity.R
MD5
DESCRIPTION
man
man/plotAmpliconduo.Rd
man/figures
man/figures/discordanceDelta.png
man/ampliconfreqs.long.Rd
man/amplicons.Rd
man/site.f.Rd
man/discordance.delta.Rd
man/ampliconduo.Rd
man/AmpliconDuo-package.Rd
man/accepted.amplicons.Rd
man/filter.ampliconduo.Rd
man/filter.ampliconduo.set.Rd
man/plotORdensity.Rd
man/ampliconfreqs.Rd
man/plotAmpliconduo.set.Rd
AmpliconDuo documentation built on May 19, 2017, 4:32 p.m.