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

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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.

Author
Anja Lange [aut, cre], Daniel Hoffmann [aut]
Date of publication
2016-01-19 13:09:23
Maintainer
Anja Lange <anja.lange@uni-due.de>
License
GPL (>= 3)
Version
1.1

View on CRAN

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

Files in this package

AmpliconDuo
AmpliconDuo/NAMESPACE
AmpliconDuo/data
AmpliconDuo/data/amplicons.rda
AmpliconDuo/data/site.f.rda
AmpliconDuo/data/ampliconfreqs.long.rda
AmpliconDuo/data/ampliconfreqs.rda
AmpliconDuo/R
AmpliconDuo/R/ampliconduo.R
AmpliconDuo/R/filter.ampliconduo.set.R
AmpliconDuo/R/discordance.delta.R
AmpliconDuo/R/filter.ampliconduo.R
AmpliconDuo/R/plotAmpliconduo.set.R
AmpliconDuo/R/plotAmpliconduo.R
AmpliconDuo/R/accepted.amplicons.R
AmpliconDuo/R/plotORdensity.R
AmpliconDuo/MD5
AmpliconDuo/DESCRIPTION
AmpliconDuo/man
AmpliconDuo/man/plotAmpliconduo.Rd
AmpliconDuo/man/figures
AmpliconDuo/man/figures/discordanceDelta.png
AmpliconDuo/man/ampliconfreqs.long.Rd
AmpliconDuo/man/amplicons.Rd
AmpliconDuo/man/site.f.Rd
AmpliconDuo/man/discordance.delta.Rd
AmpliconDuo/man/ampliconduo.Rd
AmpliconDuo/man/AmpliconDuo-package.Rd
AmpliconDuo/man/accepted.amplicons.Rd
AmpliconDuo/man/filter.ampliconduo.Rd
AmpliconDuo/man/filter.ampliconduo.set.Rd
AmpliconDuo/man/plotORdensity.Rd
AmpliconDuo/man/ampliconfreqs.Rd
AmpliconDuo/man/plotAmpliconduo.set.Rd