aldex.kw {ALDEx2} | R Documentation

## Calculate the Kruskal-Wallis test and glm ANOVA statistics

### Description

`aldex.kw` calculates the expected values of the Kruskal-Wallis test and a glm ANOVA on the data returned by `aldex.clr`.

### Usage

    aldex.kw(clr, useMC = FALSE, verbose = FALSE)

### Arguments

`clr` | An `ALDEx2` object. The output of `aldex.clr`.
`useMC` | Toggles whether to use multi-core.
`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:

`kw.ep` | a vector containing the expected p-value of the Kruskal-Wallis test for each feature
`kw.eBH` | a vector containing the corresponding expected value of the Benjamini-Hochberg corrected p-value for each feature
`glm.ep` | a vector containing the expected p-value of the glm ANOVA for each feature
`glm.eBH` | a vector containing the corresponding expected value of the Benjamini-Hochberg corrected p-value for each feature

### Author(s)

Arianne Albert

### 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("A", 4), rep("B", 3), rep("C", 7))
    x <- aldex.clr(selex, conds, mc.samples=1, denom="all")
    kw.test <- aldex.kw(x)

[Package ALDEx2 version 1.20.0 Index]