aldex.ttest: Calculate Wilcoxon Rank Sum test and Welch's t-test...

In ggloor/ALDEx_bioc: Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Calculate Wilcoxon Rank Sum test and Welch's t-test statistics

Description

aldex.ttest calculates the expected values of the Wilcoxon Rank Sum test and the posterior predictive value of Welch's t-test on the data returned by aldex.clr.

Usage

aldex.ttest(clr, paired.test = FALSE, hist.plot = FALSE, verbose = FALSE)

Arguments

clr	An ALDEx2 object. The output of aldex.clr.
paired.test	Toggles whether to calculate paired tests.
hist.plot	Toggles whether to plot a histogram of p-values for the first Dirichlet Monte Carlo instance.
verbose	A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets. Applies to effect = TRUE.

Value

Returns a data.frame with the following information:

we.ep	a vector containing the the poseterior predictive p-value of Welch's t-test for each feature
we.eBH	a vector containing the corresponding expected value of the Benjamini-Hochberg corrected p-value for each feature
wi.ep	a vector containing the expected p-value of the Wilcoxon Rank Sum test for each feature
wi.eBH	a vector containing the corresponding expected value of the Benjamini-Hochberg corrected p-value for each feature

Author(s)

Greg Gloor, Michelle Pistner

References

Please use the citation given by citation(package="ALDEx2").

See Also

aldex, aldex.clr, aldex.ttest, aldex.kw, aldex.glm, aldex.effect, aldex.corr, selex

Examples

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)

ggloor/ALDEx_bioc documentation built on Oct. 31, 2023, 1:13 a.m.