This function aggregates a data set to a fixed level of a taxonomy. For example, if aggregating to the Phylum level, it would sum up the columns of x corresponding to OTUs/ASVs in that Phylum. It also adjusts the tree information (in particular A, tree, and tax) for this new smaller problem.
aggregate_to_level(x, y, A, tax, level = 7, collapse = FALSE)
| x | n by p data matrix of counts, where n is the number of samples, p is the number of OTUs/ASVs. |
|---|---|
| y | response vector of length n |
| A | p by (t_size-1) binary matrix giving tree structure (t_size is the
total number of nodes and the -1 is because we do not include the root). This
is created by the function |
| tax | a tax table, which is a p by number-of-levels matrix, where cell ij gives the name of the level j ancestor of OTU/ASV i. |
| level | which level are we aggregating to? |
| collapse |