Agglomerate taxmap Objects

A function similar to the phyloseq::tax_glom function, that assembles abundance data at a specified rank. This removes subtaxa and reassigns the values at the specified rank.

agglomerate_taxmap(obj, rank, validated = FALSE)

Arguments

obj

A Taxmap object.

rank

The rank that will be agglomerated to.

validated

This parameter provides a way to override validation steps. Use carefully. Default: FALSE

Value

A taxmap object that has been agglomerated at the specified rank.

Details

This function helps analyzing taxonomic data at intermediate ranks by agglomerating the observation data and the taxmap object.

See also

filter_taxa

validate_MicrobiomeR_format

Other Advanced Metacoder Filters: cov_filter(), otu_prevalence_filter(), otu_proportion_filter(), taxa_prevalence_filter()

Examples

if (FALSE) { # \dontrun{
if(interactive()){
# This example uses data that are no longer available in the MicrobiomeR package,
# however, they can be easily generated with \code{\link{MicrobiomeR}{as_basic_format}}.
library(MicrobiomeR)
basic_silva <- as_MicrobiomeR_format(MicrobiomeR::raw_silva_2, "basic_format")
phylum_obj <- agglomerate_taxmap(obj = basic_silva, rank = "Phylum")
class_obj <- agglomerate_taxmap(obj = basic_silva, rank = "Class")
order_obj <- agglomerate_taxmap(obj = basic_silva, rank = "Order")
 }
} # }