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man/contaslayer.Rd

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