Description Usage Arguments Details Value
Allows subsetting of a phyloseq object according to the relative abundance of OTUs in a minimal number of samples. Returns a logical vector of OTUs that are at least n% of the sequences in at leas m samples.
1 | prop_filter(x, n, m)
|
x |
A phyloseq object. |
n |
Minimum percentage to keep OTU. |
m |
Minimum number of samples. |
The functions creates a logical vector to be used in subsetting a phyloseq object acording to the relative abundance of OTUs in a given nuber of samples. For example, if n = 1 and m = 2, then the OTUs to be kept must represent at least 1% of the sequences in at least 2 samples. The vector is then used as an argument to the phyloseq object 'prune_taxa'.
A logical vector of OTUs to keep.
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