fitDM: fitDM

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

fitDM

Description

Fit a Dirichlet-Multinomial (DM) distribution for each taxon of the count data. The model estimation procedure is performed by MGLM MGLMreg function without assuming the presence of any group in the samples (design matrix equal to a column of ones.)

Usage

fitDM(object, assay_name = "counts", verbose = TRUE)

Arguments

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

Value

A data frame containing the continuity corrected logarithms of the average fitted values for each row of the matrix of counts in the Y column, and the estimated probability to observe a zero in the Y0 column.

Examples

# Generate some random counts
counts = matrix(rnbinom(n = 60, size = 3, prob = 0.5), nrow = 10, ncol = 6)

# Fit model on the counts matrix
DM <- fitDM(counts)
head(DM)

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