44 lines
1.3 KiB
R
44 lines
1.3 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/taxonomic.resolution.R
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\name{summary.taxores}
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\alias{summary.taxores}
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\title{Dataset taxonomic resolution summary.}
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\usage{
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\method{summary}{taxores}(x, colranks, colscores, thresh = 0.7)
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}
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\arguments{
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\item{x}{a \code{\link{metabarcoding.data}} object}
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\item{colranks}{a string indicating column name where ranks are stored in \code{x}}
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\item{colscores}{a string indicating column name where taxonomic identification scores are stored in \code{x}}
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\item{thresh}{a threshold for defining at which taxonomic identification scores a sequence can be considered as "not assigned".
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Default is \code{0.7}}
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}
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\value{
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returns a data.frame and piecharts of the number/proportion of MOTUs/reads assigned to each taxonomic levels
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}
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\description{
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Summarizes the taxonomic relution of reads and MOTUs over the entire dataset
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}
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\examples{
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data(termes)
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taxo=default.taxonomy()
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termes.taxo.table = get.classic.taxonomy(termes, taxo, "taxid")
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attr(termes, "motus") = data.frame(termes$motus, termes.taxo.table)
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attr(termes, "motus")["count"] = colSums(termes$reads)
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summary.taxores(termes, "taxonomic_rank_ok","best_identity")
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}
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\seealso{
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\code{\linkS4class{taxonomy.obitools}}, and method \code{\link{taxonmicank}}
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}
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\author{
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Lucie Zinger
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}
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\keyword{taxonomy}
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