Hi,
Thank you very much for devoloping ANCOMBC2, it is a wonderful package. Although here you have uploaded detailed tutorial in Github and Bioconductor, I still have some question about contrast matrix setting in trend test.
I‘m working on a microbiota dataset with three groups (A, B, C), each group has 30+ samples. Now I want to find some microbiota taxons which have specific pattern in these groups using trend test of ANCOMBC. It is easy for detecting taxon which have monotonic trendency (increasing or decreasing) between these three groups, because it have detailed code in example. but for testing umbrella shape (convex and concave), i didn't find any example for setting contrast matrix.
Here is a code i want to test convex umbrella shape. If B is reference, I need to test B>A and B>Cmatrix(c(-1, 0, -1, 1),nrow = 2, byrow = TRUE) and setting node = 1
Is it right? Could you kindly give me some advice for testing umbrella shape if this code is not right?
Thanks,
Nemo
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