aldex.glm {ALDEx2} | R Documentation

## Calculate glm test statistics using a `model.matrix`

### Description

`aldex.glm` calculates the expected values for each coefficient of a glm model on the data returned by `aldex.clr`. This function requires the user to define a model with `model.matrix`.

### Usage

    aldex.glm(clr, verbose = FALSE, ...)

### Arguments

`clr` | An `ALDEx2` object. The output of `aldex.clr`.
`verbose` | A boolean. Toggles whether to print diagnostic information while running. Useful for debugging errors on large datasets. Applies to `effect = TRUE`.
`...` | Arguments passed to `glm`.

### Value

Returns a data.frame of the average coefficients and their p-values for each feature, with FDR appended as a `BH` column.

### Author(s)

Thom Quinn

### 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,]
    covariates <- data.frame("A" = sample(0:1, 14, replace = TRUE),
                             "B" = c(rep(0, 7), rep(1, 7)))
    mm <- model.matrix(~ A + B, covariates)
    x <- aldex.clr(selex, mm, mc.samples=1, denom="all")
    glm.test <- aldex.glm(x)

[Package ALDEx2 version 1.18.0 Index]