phyloseq_import_mothur: Create a phyloseq file from mothur database file

In vaulot/dvutils: A set of utilities

Description

Write out 3 files:

• phyloseq object as a rds file: extension .rds

• fasta sequences (unaligned): extension .fas

• fasta sequences (aligned): extension .aligned.fas

Usage

phyloseq_import_mothur(file_mothur, file_samples, n_taxo_levels)

Arguments

file_mothur	File created by mothur using the database function
file_samples	A tsv file with the sample metadata. There must be a column "sample_id" with the ID of the samples which should exactly matching the names of the columns in the mothur database file
n_taxo_levels	Number of taxonomic levels (e.g. 8 if using PR2)

Value

TRUE if no problem

Examples

phyloseq_import_mothur("mothur.database", "mothur_samples.tsv", 6)

vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.