ampliconduo {AmpliconDuo}  R Documentation 
Apply Fisher's Exact Tests To Two Amplicon Frequency Sets Of The Same Sample
Description
Implements Fisher's exact test to detect amplicons with significant deviating read numbers between two amplicon sets of the same sample. The pvalues of the Fisher's exact test are corrected for multiple testing by computation of the false discovery rates q. This function is intended to help identifying reads that may be the results of experimental artefacts. (The calculation can take some time depending on the size of the data sets and the computing power.)
Usage
ampliconduo(A, B = NULL, sample.names = NULL, correction = "fdr", ...)
Arguments
A 
A list or a data frame containing amplicon occurences / number of reads per amplicon (integer values). 
B 
Optional. A list or a data frame containing amplicon occurences. 
sample.names 
Optional. A vector or list of characters with names for the amplicon pairs. 
correction 
Optional. Specifies the correction method for the pvalues from Fisher's exact test.
Accepts one of the following characters: 
... 
Arguments passed to the internally called 
Details
If only A
is specified, it is assumed that the list elements 1 &
2, 3 & 4 etc. of A
are amplicon data of the same sample. In case A
and B
are specified, the ith frequency set of A
and B
are combined. For each amplicon data pair, frequencies at the corresponding
positions in the lists are assumed to belong to the same amplicon. It is required, that two frequency sets that belong to the same sample, an ampliconduo, have the same length. The ampliconduo
function iterates over all amplicon pairs and performs the following tasks:

amplicons with frequency zero in both samples are removed. Position information is retained.

For each amplicon Fisher's exact test using the method
fisher.test
is performed. The pvalue, odds ratio and confidence interval are returned. Via the...
, argumentsconf.level
,or
andalternative
can be passed to thefisher.test
function call. Default values areconf.level
= 0.95,or
= 1 andalternative
= "two.sided". 
The pvalues are corrected using the
p.adjust
function. By default the method by Benjamini & Hochberg (1995) is used. Setting thecorrection
argument to any of the following characters"holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
, the adjustment method for the pvalues can be changed. See functionp.adjust
.
The AmpliconDuo package implements further methods to visualize and filter the returned ampliconduo data frames.
Value
A list of data frames, one for each amplicon pair, that will be called ampliconduo data frame in the following. List entries are named according to the specified sample.names
or numbered.
Each ampliconduo data frame has 9 columns

freqA: frequencies of amplicon set A

freqB: frequencies of amplicon set B (taken from argument
B
if specified) 
p: pvalues calculated with Fisher's exact test

OR: odds ratio calculated with Fisher's exact test

CI.low: lower confidence limit for
OR

CI.up: upper confidence limit for
OR

rejected: logical, indicating whether the amplicon was rejected

sample: sample name taken from
sample.name
if specified, same for all rows in a given data frame
Author(s)
Anja Lange and Daniel Hoffmann
References
Y Benjamini and Y Hochberg. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. Series B (Methodological), 57(1):289300, 1995.
See Also
fisher.test
, used to calculate the pvalue, odds ratio and confidence interval;
p.adjust
, called to correct the pvalues;
methods to visualize or further manipulate the ampliconduo data frames:
plotAmpliconduo.set
,
plotAmpliconduo
,
discordance.delta
,
Examples
## loads read numbers from example amplicon data sets
data(ampliconfreqs)
data(site.f)
## generate ampliconduo data frames
ampliconduos.a < ampliconduo(A = ampliconfreqs[,1:4], sample.names = site.f[1:2])
ampliconduos.b < ampliconduo(A = ampliconfreqs[c(1,3)],
B = ampliconfreqs[c(2,4)], sample.names = site.f[1:2],
conf.level = 0.9)
## frequency plot
plotAmpliconduo.set(ampliconduos.a)