fitZINB {benchdamic} | R Documentation |
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.)
fitZINB(counts, verbose = TRUE)
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 |
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.
# 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)