discordance.delta {AmpliconDuo} | R Documentation |
Measure Of Discordance Between Two Amplicon Data Sets
Description
Calculates delta () and delta prime (
), the fraction of amplicon frequencies and amplicons, respectively, with a false discovery rate below a certain threshold
as a measure of discordance between two amplicon data sets A and B.
Usage
discordance.delta(x, names = NULL, theta = 0.05, corrected = TRUE,
printToTex = FALSE, directory = NULL, file.name = NULL)
Arguments
x |
A list of amplicon duo data frames as returned by the |
names |
Optional. Vector or list of characters specifying the sample/amplicon pair names. By default
names are taken from the element names of |
theta |
Optional. Numeric, threshold for the false discovery rate. Default value is 0.05. |
corrected |
Optional. Logical, indicates whether the p-value from Fisher's exact test (FALSE) or the
adjusted p-value (TRUE), here called q, is used for calculation of |
printToTex |
Optional. Logical, if |
directory |
Optional. If |
file.name |
Optional. If |
Details
Calculates and
, the fraction of frequencies of amplicons and amplicons, respectively, with false discovery rate below a certain threshold
as a measure of discordance between two amplicon data sets A and B with occurence
of amplicon i in amplicon set A of sample S (the ampliconduo data frame).
and
are defined as follows:
for number of amplicons detected in sample/ampliconduo S.
and
are located between 0 (no discordance, i.e. no statistically significant deviations between experimental branches) and 1 (complete discordance).
x
is the return value of a ampliconduo
call.
Value
Data frame with three columns. The first column contains the sample/amplicon pair names. Second and third column
harbor the corresponding and
values, respectively.
Author(s)
Anja Lange & Daniel Hoffmann
See Also
ampliconduo
, generates the expected data format for x
xtable
, used to convert the returned data frame into a Latex
table.
Examples
## load example ampliconduo data frame
data(amplicons)
## calculate the discordance between amplicon data sets of an ampliconduo data frame
dd.a <- discordance.delta(amplicons)
dd.b <- discordance.delta(amplicons, theta = 0.1)