fitDM {benchdamic} | R Documentation |
Fit a Dirichlet-Multinomial (DM) distribution for each taxon of the count
data. The model estimation procedure is performed by MGLM
MGLMreg
function without assuming the presence of any group in
the samples (design matrix equal to a column of ones.)
fitDM(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 DM <- fitDM(counts) head(DM)