aldex.ttest {ALDEx2} | R Documentation

## 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 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 expected 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

### 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)

[Package ALDEx2 version 1.20.0 Index]