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 for the RDP trainset .fa file The RDP trainset data was downloaded from: https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/

Description

## RDP Trainset 18 path <- "~/Desktop/RDP/RDPClassifier_16S_trainsetNo18_rawtrainingdata" dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset18_062020.fa"), file.path(path, "trainset18_db_taxid.txt"), "~/tax/rdp_train_set_18.fa.gz") dada2:::tax.check("~/tax/rdp_train_set_18.fa.gz", "~/Desktop/ten_16s.100.fa")

Usage

makeTaxonomyFasta_RDP(fin, fdb, fout, compress = TRUE)

Details

## RDP Trainset 16 path <- "~/Desktop/RDP/RDPClassifier_16S_trainsetNo16_rawtrainingdata" dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset16_022016.fa"), file.path(path, "trainset16_db_taxid.txt"), "~/tax/rdp_train_set_16.fa.gz")

benjjneb/dada2 documentation built on Feb. 1, 2024, 10:50 p.m.