TaxaIden_fn: Workflow Hub for Automated Metagenomic Exploration (WHAM!)

In zc1286/Wham: Workflow Hub for Automated Metagenomic Exploration (WHAM!)

Description

check the format of taxainfo and output taxa.LEVEL

Usage

TaxaIden_fn(TaxaInfo, taxa.level = c("k", "p", "o", "c", "f", "g", "s", "otu"))

Arguments

TaxaInfo	a vector store taxonomic information
taxa.level	required, c("k","p","o","c","f","g","s"). Collapsing the count to provided taxonomic level. options are "k","p","c","o","f","g","s".Only need to declaimed when argument DE is setup as "taxa". Every taxonimic level has to have "k__","p__","c__","o__","f__","g__",or "s__"

Value

a character vector corresponds with taxa.level

Examples

taxainfo = c("Unclassified",
             "k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales",
             "k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae")
TaxaIden_fn(taxainfo,taxa.level = "f")

zc1286/Wham documentation built on May 14, 2021, 8 p.m.