DA_basic: DA_basic

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

DA_basic

Description

Fast run for basic differential abundance detection methods such as wilcox and t tests.

Usage

DA_basic(
  object,
  assay_name = "counts",
  pseudo_count = FALSE,
  contrast = NULL,
  test = c("t", "wilcox"),
  paired = FALSE,
  verbose = TRUE
)

Arguments

object	a phyloseq or TreeSummarizedExperiment object.
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).
verbose	an optional logical value. If TRUE, information about the steps of the algorithm is printed. Default verbose = TRUE.

Value

A list object containing the matrix of p-values 'pValMat', a matrix of summary statistics for each tag 'statInfo', and a suggested 'name' of the final object considering the parameters passed to the function.

See Also

DA_Seurat for a similar implementation of basic tests.

Examples

set.seed(1)
# Create a very simple phyloseq object
counts <- matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6)
metadata <- data.frame("Sample" = c("S1", "S2", "S3", "S4", "S5", "S6"),
                       "group" = as.factor(c("A", "A", "A", "B", "B", "B")))
ps <- phyloseq::phyloseq(phyloseq::otu_table(counts, taxa_are_rows = TRUE),
                         phyloseq::sample_data(metadata))
# Differential abundance
DA_basic(object = ps, pseudo_count = FALSE, contrast = c("group", "B", "A"),
    test = "t", verbose = FALSE)

mcalgaro93/benchdamic documentation built on Nov. 28, 2024, 2:16 p.m.