44 lines
1.4 KiB
R
44 lines
1.4 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/taxonomy_classic_table.R
|
|
\name{get.classic.taxonomy}
|
|
\alias{get.classic.taxonomy}
|
|
\title{Get classical taxonomy format}
|
|
\usage{
|
|
get.classic.taxonomy(x, taxonomy, coltaxid)
|
|
}
|
|
\arguments{
|
|
\item{x}{a \code{\link{metabarcoding.data}} object}
|
|
|
|
\item{taxonomy}{a instance of \code{\linkS4class{taxonomy.obitools}}}
|
|
|
|
\item{coltaxid}{a the name of the column containing taxids to be used for creating classical taxonomic description}
|
|
}
|
|
\value{
|
|
returns a data.frame with the classical taxonomic description ("kingdom", "phylum", "class", "order", "family", "genus", "species"), as well as
|
|
sequence taxonomic assignment rank and scientific name for each sequences stored in the \code{\link{metabarcoding.data}} object
|
|
}
|
|
\description{
|
|
Creates a table with the classical taxonomic description (from phylum to species)
|
|
}
|
|
\examples{
|
|
|
|
data(termes)
|
|
|
|
taxo=default.taxonomy()
|
|
|
|
termes.taxo.table = get.classic.taxonomy(termes, taxo, "taxid")
|
|
head(termes.taxo.table)
|
|
|
|
attr(termes, "motus") = data.frame(termes$motus, termes.taxo.table)
|
|
|
|
|
|
}
|
|
\seealso{
|
|
\code{\linkS4class{taxonomy.obitools}}, and methods \code{\link{species}},\code{\link{genus}}, \code{\link{family}},\code{\link{kingdom}},
|
|
\code{\link{superkingdom}},\code{\link{taxonatrank}}, \code{\link{taxonmicank}}
|
|
}
|
|
\author{
|
|
Lucie Zinger
|
|
}
|
|
\keyword{taxonomy}
|