parse_silva_tax_batch: Split vector of SILVA taxonomic annotations and prepare...

View source: R/parse_silva.R

parse_silva_tax_batchR Documentation

Split vector of SILVA taxonomic annotations and prepare taxonomy table.

Description

Split vector of SILVA taxonomic annotations and prepare taxonomy table.

Usage

parse_silva_tax_batch(x, db)

Arguments

x

Vector of character strings with taxonomic annotation (assigned by BLAST)

db

Data frame with rank designations for all taxonomic paths in the SILVA taxonomy

Value

Data frame with OTUs or species as rows and their taxonomic ranks as columns.

See Also

parse_silva_tax

Examples

# Download taxonomic rank designations for all taxonomic paths used in the SILVA taxonomies
tax.db <- read.delim("https://www.arb-silva.de/fileadmin/silva_databases/release_128/Exports/taxonomy/tax_slv_ssu_128.txt", header = F, stringsAsFactors = F)
colnames(tax.db) <- c("path", "taxid", "rank", "remark", "release")

x <- c("Eukaryota;Opisthokonta;Holozoa;Metazoa (Animalia);Eumetazoa;Bilateria;Platyhelminthes;Catenulida;Catenulidae;Paracatenula galateia",
"Eukaryota;SAR;Rhizaria;Cercozoa;Imbricatea;Silicofilosea;Euglyphida;Assulinidae;Assulina;Assulina muscorum",
"Eukaryota;Opisthokonta;Nucletmycea;Fungi;Cryptomycota;LKM11;uncultured eukaryote",
"Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Basidiomycota;Ustilaginomycotina;Exobasidiomycetes;Malasseziales;Incertae Sedis;Malassezia;Malassezia restricta CBS 7877",
"Eukaryota;Opisthokonta;Nucletmycea;Fungi;Cryptomycota;LKM11;uncultured fungus",
"Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Conthreep;Oligohymenophorea;Peritrichia;Telotrochidium;uncultured eukaryote",
"No blast hit", "Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Armophorea;Armophorida;Metopus;Metopus striatus",
"Eukaryota;Opisthokonta;Holozoa;Metazoa (Animalia);Eumetazoa;Bilateria;Rotifera;Monogononta;Ploimida;Lepadella patella",
"Eukaryota;SAR;Rhizaria;Cercozoa;Novel Clade 10;uncultured eukaryote"
)
parse_silva_tax_batch(x, tax.db)


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