View source: R/fitDistribution.R
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,
epsilon = 1e10, and not assuming the presence
of any group in the samples (design matrix equal to a column of ones.)
fitZINB(object, assay_name = "counts", verbose = TRUE)
a phyloseq object, a TreeSummarizedExperiment object, or a matrix of counts.
the name of the assay to extract from the
TreeSummarizedExperiment object (default
an optional logical value. If
A data frame containing the continuity corrected logarithms of the
average fitted values for each row of the matrix of counts in the
column, and the estimated probability to observe a zero in the
# 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)
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