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()

Value

The result of ALDEx2::aldex()

Details

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

Author

Adrien Taudière

Examples

res_aldex <- aldex_pq(data_fungi_mini,
  bifactor = "Height",
  modalities = c("Low", "High")
)
#> aldex.clr: generating Monte-Carlo instances and clr values
#> conditions vector supplied
#> operating in serial mode
#> aldex.scaleSim: adjusting samples to reflect scale uncertainty.
#> aldex.ttest: doing t-test
#> aldex.effect: calculating effect sizes
ALDEx2::aldex.plot(res_aldex, type = "volcano")