Subset species by taxonomic expression
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.
subset_taxa(physeq, ...)
physeq |
A |
... |
The subsetting expression that should be applied to the
|
A subsetted object with the same class as physeq.
## ex3 <- subset_taxa(GlobalPatterns, Phylum=="Bacteroidetes")
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