fitNB: fitNB

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

fitNB

Description

Fit a Negative Binomial (NB) distribution for each taxon of the count data. The NB estimation procedure is performed by edgeR glmFit function, using TMM normalized counts, tag-wise dispersion estimation, and not assuming the presence of any group in the samples (design matrix equal to a column of ones).

Usage

fitNB(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 'counts' matrix 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 matrix of counts
NB <- fitNB(counts)
head(NB)

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