parse_taxonomy_amptk: Parse taxonomy string from AMPtk (for single OTU)

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Parse taxonomy string from AMPtk (for single OTU)

Description

Parse taxonomy string from AMPtk (for single OTU)

Usage

parse_taxonomy_amptk(x, custom_ranks = NULL)

Arguments

x	Character vector of length 1 with taxonomic annotation of single OTU/species.
custom_ranks	Named vector with customized prefixes for taxonomic ranks

Details

This function will split

Value

Named character vector with taxonomic ranks of OTU or species.

References

AMPtk: Amplicon ToolKit for NGS data (formally UFITS): https://github.com/nextgenusfs/amptk

See Also

parse_taxonomy_qiime

Examples

parse_taxonomy_amptk("k:Fungi,p:Zygomycota,o:Mortierellales,f:Mortierellaceae,g:Mortierella,s:Mortierella parvispora")
parse_taxonomy_amptk("k:Fungi,p:Ascomycota,g:Chalara")

# With customized ranks
parse_taxonomy_amptk(
 x = "do:Eukaryota,su:Amorphea,cd:Obazoa,gr:Opisthokonta,sg:Holomycota(Nucletmycea),ki:Fungi,sk:Dikarya,ph:Ascomycota,sd:Saccharomycotina,cl:Saccharomycetes,sc:Saccharomycetidae,or:Saccharomycetales,fa:Saccharomycetaceae,ge:Saccharomyces,sp:Saccharomyces cerevisiae,st:Saccharomyces cerevisiae var boulardii",
 custom_ranks = c(do = "Domain", su = "Supergroup", cd = "Clade", gr = "Group", sg = "Subgroup", ki = "Kingdom", sk = "Subkingdom", ph = "Phylum", sd = "Subdivision", cl = "Class", sc = "Subclass", or = "Order", fa = "Family", ge = "Genus", sp = "Species", st = "Strain"))

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