set_basic: set_basic

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

set_basic

Description

Set the parameters for basic differential abundance detection methods such as t and wilcox.

Usage

set_basic(
  assay_name = "counts",
  pseudo_count = FALSE,
  contrast = NULL,
  test = c("t", "wilcox"),
  paired = FALSE,
  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	add 1 to all counts if TRUE (default pseudo_count = FALSE).
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.
test	name of the test to perform. Choose between "t" or "wilcox".
paired	boolean. Choose whether the test is paired or not (default paired = FALSE). If paired = TRUE be sure to provide the object properly ordered (by the grouping variable).
expand	logical, if TRUE create all combinations of input parameters (default expand = TRUE).

Value

A named list containing the set of parameters for DA_basic method.

See Also

DA_basic

Examples

# Set some basic methods
basic_methods <- set_basic(pseudo_count = FALSE, test = c("t", "wilcox"),
    contrast = c("group", "B", "A"), expand = TRUE)

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