53 lines
1.9 KiB
R
53 lines
1.9 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/metabarcoding_threshold.R
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\docType{methods}
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\name{threshold.mask,metabarcoding.data-method}
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\alias{threshold.mask,metabarcoding.data-method}
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\alias{threshold.mask-methods,metabarcoding.data}
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\title{Computes a cumulatif thresold mask for filtering read aboundancies.}
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\usage{
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\S4method{threshold.mask}{metabarcoding.data}(data, MARGIN, threshold = 0.97,
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operator = "<")
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}
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\arguments{
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\item{data}{The \code{\linkS4class{metabarcoding.data}} instance
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on normalisation have to be computed.}
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\item{MARGIN}{Indicates if the sums have to be computed across
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samples or motus.
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Allowed values are :
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\itemize{
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\item{'sample' or 1} for computing sum across samples
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\item{'motu' or 2} for computing sum across motus
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}}
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\item{threshold}{a numeric value between 0 and 1 indicating which part of
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the signal must be conserved. Default value is setup to
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0.97 (97% of the total signal).}
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\item{operator}{is a logical comparison operator.}
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}
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\value{
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A logical matrix usable for selecting cell in the read aboundancy matrix.
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}
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\description{
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The method \code{threshold.mask} of the class \code{\linkS4class{metabarcoding.data}}
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computes a logical matrix of the same size than the read matrix of the data parameter.
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Each cell of this matrix contains a \code{TRUE} or a \code{FALSE} value according to the
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relationship existing between the read abondancy and the corresponding theshold as computed
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by the \code{\link{theshold}} method.
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}
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\details{
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(computed value) = (read aboundancy) operator (threshold value)
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for a cell in the result matrix, \code{(read aboundancy)} is extracted from the read layer.
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\code{operator} is a comparaison operator and \code{(threshold value)} is estimated with the
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\code{\link{theshold}} method.
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}
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\seealso{
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\code{\linkS4class{metabarcoding.data}}, \code{\link{threshold.mask}}, \code{\link{threshold}}
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}
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\author{
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Aurelie Bonin
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}
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