makeTaxonomyFasta_RDP: This function creates the dada2 assignTaxonomy training fasta...

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

This function creates the dada2 assignTaxonomy training fasta from the speciesrank RDP trainset .fa file The RDP trainset data was downloaded from: https://sourceforge.net/projects/rdp-classifier/

Description

## RDP Trainset 19 path <- "~/tax/rdp/v19" dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset19_072023_speciesrank.fa"), file.path(path, "trainset19_db_taxid.txt"), "~/Desktop/rdp_19_toGenus_trainset.fa.gz", include.species=FALSE, compress=TRUE) dada2:::tax.check("~/Desktop/rdp_19_toGenus_trainset.fa.gz")

Usage

makeTaxonomyFasta_RDP(fin, fdb, fout, include.species = FALSE, compress = TRUE)

Details

dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset19_072023_speciesrank.fa"), file.path(path, "trainset19_db_taxid.txt"), "~/Desktop/rdp_19_toSpecies_trainset.fa.gz", include.species=TRUE, compress=TRUE) dada2:::tax.check("~/Desktop/rdp_19_toSpecies_trainset.fa.gz")

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.