61 lines
2.4 KiB
R
61 lines
2.4 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/choose.taxonomy.R
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\name{taxo.decider}
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\alias{taxo.decider}
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\title{Choose between databases for taxonomic classifications}
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\usage{
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taxo.decider(x, taxonomy, dbrank, thresh = 0.95)
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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{taxonomy}{a \code{\linkS4class{taxonomy.obitools}} instance}
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\item{dbrank}{string or vector indicating reference database names ranked by order of preference}
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\item{thresh}{a best_identity threshold for applying priority. Default is \code{0.95}}
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}
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\value{
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returns a data.frame with the refined taxonomic assignement and classic taxonomy description.
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}
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\description{
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Chooses a sequence taxonomic assignment in order of preference for the different
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reference databases that have been used when the assignment is above a certain threshold
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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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#create artificial taxonomic assignments
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attr(termes, "motus")["best_identity:DB1"] = sample(seq(0.5,1,0.001),size=nrow(termes$motus), replace=T)
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attr(termes, "motus")["best_identity:DB2"] = sample(seq(0.5,1,0.001),size=nrow(termes$motus), replace=T)
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attr(termes, "motus")["best_identity:DB3"] = sample(seq(0.5,1,0.001),size=nrow(termes$motus), replace=T)
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attr(termes, "motus")["taxid_by_db:DB1"] = termes$motus$taxid
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attr(termes, "motus")["taxid_by_db:DB2"] = sample(termes$motus$taxid,size=nrow(termes$motus), replace=F)
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attr(termes, "motus")["taxid_by_db:DB3"] = sample(termes$motus$taxid,size=nrow(termes$motus), replace=F)
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#Run taxo.decider
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termes.ok = taxo.decider(termes, taxo, "DB2", 0.95)
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head(termes.ok$motus[union(grep("DB", colnames(termes.ok$motus)), grep("_ok", colnames(termes.ok$motus)))])
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termes.ok = taxo.decider(termes, taxo, c("DB3", "DB1"), 0.95)
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head(termes.ok$motus[union(grep("DB", colnames(termes.ok$motus)), grep("_ok", colnames(termes.ok$motus)))])
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#Quick look at the enhancement in taxonomic assignements
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par(mfrow=c(1,4))
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for(i in grep("best_identity.", colnames(termes.ok$motus))){
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hist(termes.ok$motus[,i], breaks=20, ylim=c(1,21), main=colnames(termes.ok$motus)[i], xlab="assignment score")
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}
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}
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\seealso{
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\code{\linkS4class{taxonomy.obitools}}, and methods \code{\link{species}},\code{\link{genus}}, \code{\link{family}},\code{\link{kingdom}},
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\code{\link{superkingdom}},\code{\link{taxonatrank}}, \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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