set_mixMC: set_mixMC

In mcalgaro93/benchdamic: Benchmark of differential abundance methods on microbiome data

set_mixMC

Description

Set the parameters for mixMC sPLS-DA.

Usage

set_mixMC(
  assay_name = "counts",
  pseudo_count = 1,
  contrast = NULL,
  ID_variable = NULL,
  expand = TRUE
)

Arguments

assay_name	the name of the assay to extract from the TreeSummarizedExperiment object (default assayName = "counts"). Not used if the input object is a phyloseq.
pseudo_count	a positive numeric value for the pseudo-count to be added. Default is 1.
contrast	character vector with exactly, three elements: a string indicating the name of factor whose levels are the conditions to be compared, the name of the level of interest, and the name of the other level.
ID_variable	a character string indicating the name of the variable name corresponding to the repeated measures units (e.g., the subject ID).
expand	logical, if TRUE create all combinations of input parameters (default expand = TRUE).

Value

A named list contaning the set of parameters for DA_mixMC method.

See Also

DA_mixMC

Examples

# Set some basic combinations of parameters for mixMC
base_mixMC <- set_mixMC(pseudo_count = 1, contrast = c("group", "B", "A"))
many_mixMC <- set_mixMC(pseudo_count = c(0.1, 0.5, 1), 
    contrast = c("group", "B", "A"))

mcalgaro93/benchdamic documentation built on March 10, 2024, 10:40 p.m.