run_DA runs a set of predefined differential abundance methods on a
phyloseq object. This function includes normalization, calculation of matrix
of zinbweights, and running of the DA methods.
run_DA(object, conditions_col, conditions, verbose = FALSE)A phyloseq object.
A character string indicating the name of the column in sample_metadata that contains the conditions to be compared.
A named character vector. The names must be
"condB" and "condA". condB indicates the reference/numerator/control
and condA indicates the target/denominator/treatment. For example:
c(condB = 'control', condA = 'treatment')
This argument is passed to the
runNormalizations and
runDA functions.
A list containing the results of the DA methods. The output is compatible with the benchdamic framework.