parse_amplicon_table: Parse amplicon table

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Parse amplicon table

Description

Parse amplicon table

Usage

parse_amplicon_table(
  amp = otu.tab,
  tax = blast,
  tax_type = "BLAST",
  add.tax.to.data = TRUE,
  tax.db
)

Arguments

amp	File name with OTU table (generated with VSEARCH or USEARCH)
tax	File name with OTU taxonomic annotations
tax_type	Type of taxonomic annotation ("BLAST", "SINA", "STAMPA")
add.tax.to.data	logical, add taxonomic annotations to the OTU table?
tax.db	SILVA database with taxonomy strings and corresponding tax ranks (e.g. tax_slv_ssu_128.txt)

Value

list

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.