aldex_pq: Run Aldex on a phyloseq object

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Run Aldex on a phyloseq object

Description

Run Aldex on a phyloseq object

Usage

aldex_pq(physeq, bifactor = NULL, modalities = NULL, gamma = 0.5, ...)

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
bifactor	(required) The name of a column present in the ⁠@sam_data⁠ slot of the physeq object. Must be a character vector or a factor.
modalities	(default NULL) A vector of modalities to keep in the analysis. If NULL, all modalities present in bifactor are kept. Note that only two modalities are allowed.
gamma	(default 0.5) The value of the Dirichlet Monte-Carlo sampling parameter.
...	Additional arguments passed on to ALDEx2::aldex()

Details

It is a wrapper of the ALDEx2::aldex() function with default gamma=0.5.

Value

The result of ALDEx2::aldex()

Author(s)

Adrien Taudière

Examples

if (requireNamespace("ALDEx2")) {
  res_aldex <- aldex_pq(data_fungi_mini,
    bifactor = "Height",
    modalities = c("Low", "High")
  )
  ALDEx2::aldex.plot(res_aldex, type = "volcano")
}

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.