DA_MAST: DA_MAST

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

DA_MAST

Description

Fast run for MAST differential abundance detection method.

Usage

DA_MAST(
  object,
  assay_name = "counts",
  pseudo_count = FALSE,
  rescale = c("median", "default"),
  design,
  coefficient = NULL,
  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).
rescale	Rescale count data, per million if 'default', or per median library size if 'median' ('median' is suggested for metagenomics data).
design	The model for the count distribution. Can be the variable name, or a character similar to "~ 1 + group", or a formula, or a 'model.matrix' object.
coefficient	The coefficient of interest as a single word formed by the variable name and the non reference level. (e.g.: 'ConditionDisease' if the reference level for the variable 'Condition' is 'control').
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', the 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

zlm for the Truncated Gaussian Hurdle model estimation.

Examples

set.seed(1)
# Create a very simple phyloseq object
counts <- matrix(rnbinom(n = 600, size = 3, prob = 0.5), 
                 nrow = 100, 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_MAST(object = ps, pseudo_count = FALSE, rescale = "median",
    design = ~ group, coefficient = "groupB")

mcalgaro93/benchdamic documentation built on Sept. 26, 2024, 6:34 p.m.