Collapse taxa in a microbiome_dataset to a taxonomy rank.
Usage
agglomerate_taxa(
object,
taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
what = c("sum_intensity", "mean_intensity", "median_intensity"),
na_remove = TRUE
)
Arguments
- object
A microbiome_dataset object.
- taxonomic_rank
A taxonomy rank in variable_info.
- what
Aggregation method.
- na_remove
Should taxa with missing rank be removed before agglomeration?
Value
A microbiome_dataset object.
Examples
data("global_patterns", package = "microbiomedataset")
x <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:200])
x <- agglomerate_taxa(
object = x,
taxonomic_rank = "Genus",
what = "sum_intensity"
)
dim(x@expression_data)
#> [1] 19 26
