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]