Raw counts of genera were used as input to the ANCOM.main function from the ANCOM v 2 R code (downloaded from https://sites.google.com/site/siddharthamandal1985/research). PD vs control was specified as the main variable. The taxa-wise FDR option (multcorr = 2) was chosen for the multiple testing correction method. An FDR significance threshold of 0.05 was chosen for calculation of W statistics. W statistics greater than or equal to 80% of the total number of genera tested were considered significant.
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