View source: R/fitDistribution.R
Fit a Negative Binomial (NB) distribution for each taxon of the count data.
The NB estimation procedure is performed by edgeR
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).
fitNB(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 'counts' matrix in the 'Y' column, and the estimated probability to observe a zero in the 'Y0' column.
# 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)
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