subset_samples: Subset samples by sample_data expression
Description
This is a convenience wrapper around the
subset function. It is intended to allow
subsetting complex experimental objects with one function
call. Subsetting is based on an expression for which the
context first includes the variables contained in
sample_data. The samples retained in
the dataset is equivalent to x[subset &
!is.na(subset)], where x is the vector of sample
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 samples that have a missing
value, NA, somewhere in the expression.
Usage
subset_samples(physeq, ...)
Arguments
physeq
A sample_data-class, or a
phyloseq-class object with a
sample_data. If the sample_data 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 sample_data. This is passed on to
subset, see its documentation for more
details.