discordance.delta {AmpliconDuo} | R Documentation |
Calculates delta (Δ) and delta prime (Δ'), the fraction of amplicon frequencies and amplicons, respectively, with a false discovery rate below a certain threshold θ as a measure of discordance between two amplicon data sets A and B.
discordance.delta(x, names = NULL, theta = 0.05, corrected = TRUE, printToTex = FALSE, directory = NULL, file.name = NULL)
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 Δ and Δ'. |
printToTex |
Optional. Logical, if |
directory |
Optional. If |
file.name |
Optional. If |
Calculates Δ and Δ', the fraction of frequencies of amplicons and amplicons, respectively, with false discovery rate below a certain threshold θ as a measure of discordance between two amplicon data sets A and B with occurence r_{(iAS)} of amplicon i in amplicon set A of sample S (the ampliconduo data frame). Δ and Δ' are defined as follows:
for number n_S of amplicons detected in sample/ampliconduo S. Δ_{Sθ} and Δ'_{Sθ} 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.
Data frame with three columns. The first column contains the sample/amplicon pair names. Second and third column harbor the corresponding Δ and Δ' values, respectively.
Anja Lange & Daniel Hoffmann
ampliconduo
, generates the expected data format for x
xtable
, used to convert the returned data frame into a Latex
table.
## 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)