aldex.glm: Calculate glm test statistics using a 'model.matrix'
In ALDEx2: Analysis Of Differential Abundance Taking Sample Variation Into Account

Description Usage Arguments Value Author(s) References See Also Examples

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.

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

`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`.

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

Thom Quinn

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

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

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)