parse_silva_tax: Split single SILVA taxonomic annotation to taxonomic ranks.
In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis
parse_silva_tax R Documentation
Split single SILVA taxonomic annotation to taxonomic ranks.
Description
Split single SILVA taxonomic annotation to taxonomic ranks.
Usage
parse_silva_tax(x, db)
Arguments
x
Character string with taxonomic annotation from BLAST.
db
Data frame with rank designations for all taxonomic paths in the SILVA taxonomy.
Details
This function will split the taxonomic annotation based on the SILVA database and assign a corresponding taxonomic rank to the obtained parts.
Value
Named charcter vector with taxonomic annotation (names = rank designations).
See Also
parse_silva_tax_batch
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 <- "Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Conthreep;Oligohymenophorea;Peritrichia;Telotrochidium;uncultured eukaryote"
parse_silva_tax(x, tax.db)
vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.
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| parse_silva_tax | R Documentation |
Split single SILVA taxonomic annotation to taxonomic ranks.
Description
Split single SILVA taxonomic annotation to taxonomic ranks.
Usage
parse_silva_tax(x, db)
Arguments
x |
Character string with taxonomic annotation from BLAST. |
db |
Data frame with rank designations for all taxonomic paths in the SILVA taxonomy. |
Details
This function will split the taxonomic annotation based on the SILVA database and assign a corresponding taxonomic rank to the obtained parts.
Value
Named charcter vector with taxonomic annotation (names = rank designations).
See Also
parse_silva_tax_batch
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 <- "Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Conthreep;Oligohymenophorea;Peritrichia;Telotrochidium;uncultured eukaryote"
parse_silva_tax(x, tax.db)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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