SSU Amplicon Frequencies Of Different Sampling Sites (Short Version)

Description

A data frame with 16 amplicon data sets taken from 8 different sampling sites. A reduced version (frequencies of 2500 amplicons) of the ampliconfreqs.long data provided with this package. 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 site.f.

Usage

data(ampliconfreqs)

Format

A data frame with 80903 observations on the following 16 variables.

FU25.A

a numeric vector

FU25.B

a numeric vector

FU28.A

a numeric vector

FU28.B

a numeric vector

FU31.A

a numeric vector

FU31.B

a numeric vector

FU31.C

a numeric vector

FU31.D

a numeric vector

FU34.A

a numeric vector

FU34.B

a numeric vector

FU37.A

a numeric vector

FU37.B

a numeric vector

UniPond.A

a numeric vector

UniPond.B

a numeric vector

BogSoil.A

a numeric vector

BogSoil.B

a numeric vector

References

Lange A, Jost S, Heider D, Bock C, Budeus B, Schilling E, Strittmatter A, Boenigk J, Hoffmann D: AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities. (PLoS One. 2015 Nov 2;10(11))

Examples

data(ampliconfreqs)
data(site.f)
ampliconduo.a <- ampliconduo(ampliconfreqs[,1:4], sample.names = site.f[1:2])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(AmpliconDuo)
Loading required package: ggplot2
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/AmpliconDuo/ampliconfreqs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ampliconfreqs
> ### Title: SSU Amplicon Frequencies Of Different Sampling Sites (Short
> ###   Version)
> ### Aliases: ampliconfreqs
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ampliconfreqs)
> data(site.f)
> ampliconduo.a <- ampliconduo(ampliconfreqs[,1:4], sample.names = site.f[1:2])
..> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>