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Run LEfSe on a phyloseq object

Source: R/beta_div_test.R
lefser_pq.Rd

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. lifecycle-experimental

Author

Adrien Taudière

Examples

res_lefse <- lefser_pq(data_fungi,
  bifactor = "Height",
  modalities = c("Low", "High")
)
#> Registered S3 method overwritten by 'ggtree':
#>   method         from     
#>   fortify.igraph ggnetwork
#> The outcome variable is specified as 'Height' and the reference category is 'High'.
#>  See `?factor` or `?relevel` to change the reference category.
lefser::lefserPlot(res_lefse)
#> Warning: Ignoring unknown parameters: `size`