agg.table.taxo: Table aggregation according to taxonomy Aggregates an ASV/OTU...

In marccamb/optiranger: Optimisation of random forest for classification on microbial community data

Table aggregation according to taxonomy Aggregates an ASV/OTU table according to a given taxonomic level

Description

Table aggregation according to taxonomy Aggregates an ASV/OTU table according to a given taxonomic level

Usage

agg.table.taxo(tab, tax.lvl = "genus", tax.table)

Arguments

tab	An abundance table containing samples in columns and OTUs/ASV in rows.
tax.lvl	A string specifying the taxonomic level to be used for aggregation. tax.lvl should be the name of one colum of tax.table (case insensitive). The default is "genus".
tax.table	A table containing the taxonomy of each ASV/OTU.

Value

An abundance table with the sum of counts for each ASV/OTU corresponding to a given taxonomic level, found in each sample. ASV/OTUs that are not assigned at this specific level are discarded.

marccamb/optiranger documentation built on June 19, 2024, 9:18 a.m.