45 lines
1.2 KiB
R
45 lines
1.2 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/contaslayer.R
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\name{contaslayer}
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\alias{contaslayer}
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\title{Detects contaminants in metabarcoding data}
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\usage{
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contaslayer(x, controls, clust = NULL)
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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{controls}{a vector of samples names where conta are suspected to be detected
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(typically negative control names).}
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\item{clust}{a vector for grouping sequences. Default set to \code{NULL}.}
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}
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\value{
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a vector containing the names of sequences identified as contaminants
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}
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\description{
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Detects sequences/motus in a \code{\link{metabarcoding.data}} object
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for which frequencies over the entire dataset are maximum in negative controls and
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hence, most likely to be contaminants.
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}
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\examples{
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data(termes)
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termes.ok = termes[,colSums(termes$reads)>0]
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neg = rownames(termes.ok)[grep("r",rownames(termes.ok))]
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#finds contaminants based on neg samples
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contaslayer(termes.ok, neg)
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# extanding contamininant detection with grouping factor,
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# typically obiclean/sumatra cluster or taxonomy membership
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contaslayer(termes.ok, neg, termes.ok$motus$scientific_name)
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}
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\seealso{
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\code{\link{threshold}} for further trimming
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}
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\author{
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Lucie Zinger
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}
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