58 lines
1.8 KiB
R
58 lines
1.8 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{normalize,metabarcoding.data-method}
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\alias{normalize,metabarcoding.data-method}
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\alias{normalize-methods,metabarcoding.data}
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\title{Normalizes read counts by sample or by MOTU.}
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\usage{
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\S4method{normalize}{metabarcoding.data}(data, MARGIN = "sample",
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as.matrix = FALSE)
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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{as.matrix}{Logical indicating if the normalized aboundancies
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must be returned as a simple \code{matrix} (TRUE) or as a new
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instance of the \code{\linkS4class{metabarcoding.data}} class
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(FALSE, the default case).}
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}
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\value{
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Returns a new instance of \code{\linkS4class{metabarcoding.data}}
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or a \code{numeric} matrix according to the \code{return.as.matrix}
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parameter.
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}
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\description{
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Method \code{normalize} computes a normalized read aboundancy matrix
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(relative frequency matrix) of a \code{\link{metabarcoding.data}} instance.
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Normalization can be done according aboundancies per sample or per MOTU.
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}
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\examples{
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# load termite data set from the ROBITools sample data
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data(termes)
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# Computes normalized aboundancies per sample
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termes.norm = normalize(termes,MARGIN="sample")
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# Computes normalized aboundancies per sample and
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# stores the result as a new layer into the thermes
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# structure
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termes$normalized = normalize(termes,MARGIN="sample",as.matrix=TRUE)
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}
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\seealso{
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\code{\linkS4class{metabarcoding.data}}
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}
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\author{
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Aurelie Bonin
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}
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