lefser_pq: Run LEfSe on a phyloseq object

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Run LEfSe on a phyloseq object

Description

Run LEfSe on a phyloseq object

Usage

lefser_pq(
  physeq,
  bifactor = NULL,
  modalities = NULL,
  compute_relativeAb = TRUE,
  by_clade = FALSE,
  ...
)

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.
compute_relativeAb	(logical, default TRUE) Do we compute relative abundance before running LEfSe?
by_clade	(logical, default FALSE) Do we use the lefserClades function (which test for different depth in the taxonomic classification) or the lefser function (taxa-level)?
...	Additional arguments passed on to lefser::lefser()

Details

It is a wrapper of the lefser::lefser() and lefser::lefserClades() functions.

Value

The result of lefser::lefser() or lefser::lefserClades()

Author(s)

Adrien Taudière

Examples

if (requireNamespace("lefser") && requireNamespace("mia")) {
  res_lefse <- lefser_pq(data_fungi_mini,
    bifactor = "Height",
    modalities = c("Low", "High")
  )
  lefser::lefserPlot(res_lefse)
}

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