Lefser method — DA_lefse • MicrobiomeBenchmarkDataAnalyses

DA_lefser is a modified version of the lefser package, which includes the pvalues of the Kruskal test.

DA_lefse(
  object,
  pseudo_count = FALSE,
  conditions,
  norm = "none",
  verbose = FALSE,
  groupCol,
  ...
)

Arguments

object: A phyloseq or (Tree)SummarizedExperiment object.
pseudo_count: Add or not a pseudocount of 1. Default is FALSE.
conditions: A named character vector of length two. Names must be "condB" and "condA" in that order. "condB" must indicate control/reference/denominator and "condA" must indicate treatment/target/numerator. Example: c(condB = 'control', condA = 'treatment')
norm: Normalization method. Options: none, CLR, and TSS.
verbose: If TRUE, messages are displayed on screen. Default is FALSE.
groupCol: Name of the column in colData with the conditions.
...: Parameters passed to lefser.

An object ready to be included in the benchdamic framework.