aldex.ttest {ALDEx2} | R Documentation |
calculates expected values of the Welch's t-test and Wilcoxon rank test on the data returned by clr_function.r
aldex.ttest(clr, conditions, paired.test = FALSE, hist.plot=FALSE)
clr |
|
conditions |
a description of the data structure to be used for testing |
paired.test |
whether the Welch's test should be paired or not |
hist.plot |
whether to plot a histogram of P values for an individual Dirichlet Monte-Carlo instance. Plot is output to the standard R plotting device. |
An explicit example for two conditions is shown in the ‘Examples’ below.
Outputs a dataframe with the following information:
we.ep |
a vector containing the expected P value of the Welch's t-test for each feature |
we.eBH |
a vector containing the expected value of the Benjamini Hochberg corrected P value for each feature |
wi.ep |
a vector containing the expected P value of the Wilcoxon test for each feature |
wi.eBH |
a vector containing the expected value of the Benjamini Hochberg corrected P value for each feature |
Greg Gloor
Please use the citation given by citation(package="ALDEx")
.
aldex.clr
,
aldex.glm
,
aldex.effect
,
selex
# x is the output of the \code{x <- aldex.clr(data, mc.samples)} function # conditions is a description of the data # for the selex dataset, conditions <- c(rep("N", 7), rep("S", 7)) data(selex) #subset for efficiency selex <- selex[1201:1600,] conds <- c(rep("NS", 7), rep("S", 7)) x <- aldex.clr(selex, conds, mc.samples=2, denom="all") ttest.test <- aldex.ttest(x, conds)