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()

Value

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

Details

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

Author

Adrien Taudière

Examples

# \donttest{
if (requireNamespace("lefser") && requireNamespace("mia")) {
  res_lefse <- lefser_pq(data_fungi_mini,
    bifactor = "Height",
    modalities = c("Low", "High")
  )
  lefser::lefserPlot(res_lefse)
}
#> Loading required namespace: lefser
#> Loading required namespace: mia
#> The outcome variable is specified as 'Height' and the reference category is 'High'.
#>  See `?factor` or `?relevel` to change the reference category.
#> No significant features found.
#> Warning: Ignoring unknown parameters: `size`

# }