Remove taxa from a microbiome_dataset while keeping
expression_data, variable_info, otu_tree, taxa_tree, and ref_seq
synchronized.
Usage
prune_taxa(object, variable_id, variable_index, keep = TRUE)
Arguments
- object
A microbiome_dataset object.
- variable_id
Variable identifiers to keep or remove.
- variable_index
Variable indices to keep or remove.
- keep
Should the provided taxa be kept? Defaults to TRUE.
Value
A microbiome_dataset object.
Examples
data("global_patterns", package = "microbiomedataset")
keep_taxa <- global_patterns@variable_info$variable_id[1:5]
x <- prune_taxa(global_patterns, variable_id = keep_taxa)
dim(x@expression_data)
#> [1] 5 26
