Subset samples by sample_data expression
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.
subset_samples(physeq, ...)
physeq |
A |
... |
The subsetting expression that should be applied to the
|
A subsetted object with the same class as physeq.
# data(GlobalPatterns) # subset_samples(GlobalPatterns, SampleType=="Ocean")
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