fitZIG {benchdamic}R Documentation

fitZIG

Description

Fit a Zero-Inflated Gaussian (ZIG) distribution for each taxon of the count data. The model estimation procedure is performed by metagenomeSeq fitZig function without assuming the presence of any group in the samples (design matrix equal to a column of ones.)

Usage

fitZIG(counts, scale = "default", verbose = TRUE)

Arguments

counts

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

scale

Character vector, either median or default to choose between the median of the library size or one thousand to scale normalization factors.

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
ZIG <- fitZIG(counts, scale = "median")
head(ZIG)

[Package benchdamic version 1.0.0 Index]