fitZINB {benchdamic} | R Documentation

## fitZINB

### Description

Fit a Zero-Inflated Negative Binomial (ZINB) distribution for each taxon of the countdata. The ZINB estimation procedure is performed by zinbwave `zinbFit` function with `commondispersion = FALSE`, regularization parameter `epsilon = 1e10`, and not assuming the presence of any group in the samples (design matrix equal to a column of ones.)

### Usage

    fitZINB(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 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
    ZINB <- fitZINB(counts)
    head(ZINB)

[Package benchdamic version 1.0.0 Index]