Implements Fisher's exact test to detect amplicons with significant deviating read numbers between two amplicon sets of the same sample. The p-values 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.)
ampliconduo(A, B = NULL, sample.names = NULL, correction = "fdr", ...)
"holm", "hochberg", "hommel",
"bonferroni", "BH", "BY","fdr"
and "none"
. Default is "fdr"
.
For more details see p.adjust
.fisher.test
function.
sample.names
or numbered.Each ampliconduo data frame has 9 columns
B
if specified)
OR
OR
sample.name
if specified, same for all rows in a given data frame
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:
fisher.test
is performed. The p-value, odds ratio and confidence interval are returned. Via the ...
, arguments
conf.level
, or
and alternative
can be passed to the fisher.test
function call. Default values are conf.level
= 0.95, or
= 1 and alternative
= "two.sided".
p.adjust
function. By default the method by Benjamini & Hochberg (1995) is used.
Setting the correction
argument to any of the following characters "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
, the adjustment method for the p-values can be changed. See function p.adjust
.
The AmpliconDuo package implements further methods to visualize and filter the returned ampliconduo data frames.
fisher.test
, used to calculate the p-value, odds ratio and confidence interval; p.adjust
, called to correct the p-values;
methods to visualize or further manipulate the ampliconduo data frames:
## 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)
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