fitNB {benchdamic}R Documentation

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(counts, verbose = TRUE)

Arguments

counts

a phyloseq object or a matrix of counts with features (OTUs, ASVs, genes) by row and samples by column.

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)

[Package benchdamic version 1.0.0 Index]