subset_taxa: Subset species by taxonomic expression
Description
This is a convenience wrapper around the
subset function. It is intended to speed
subsetting complex experimental objects with one function
call. In the case of subset_taxa, the subsetting
will be based on an expression related to the columns and
values within the tax_table (taxonomyTable
component) slot of physeq. The OTUs
retained in the dataset is equivalent to x[subset &
!is.na(subset)], where x is the vector of OTU IDs
and subset is the logical that results from your
subsetting expression. This is important to keep in mind,
as users are often unaware that this subsetting step also
removes/omits OTUs that have a missing value result,
NA, somewhere in the expression.
Usage
subset_taxa(physeq, ...)
Arguments
physeq
A taxonomyTable-class, or
phyloseq-class that contains a
taxonomyTable. If the tax_table slot is missing in
physeq, then physeq will be returned as-is
and a warning will be printed to screen.
...
The subsetting expression that should be
applied to the taxonomyTable. This is passed on to
subset, and more details and examples about
how it functions can be found in its documentation.