contaslayer.Rd 1.22 KB
 Eric Coissac committed Jul 25, 2018 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 % 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 }