fitHURDLE {benchdamic} | R Documentation |
Fit a truncated gaussian hurdle model for each taxon of the count data. The
hurdle model estimation procedure is performed by MAST zlm
function without assuming the presence of any group in the samples (design
matrix equal to a column of ones.)
fitHURDLE(counts, scale = "default", verbose = TRUE)
counts |
a phyloseq object or a matrix of counts with features (OTUs, ASVs, genes) by row and samples by column. |
scale |
Character vector, either |
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 HURDLE <- fitHURDLE(counts, scale = "median") head(HURDLE)