View source: R/aggregate_to_level.R
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.
1 | 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 |
see |
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