Commit the man pages and make aggregate public again

man/normalize-methods.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/metabarcoding_threshold.R
+\docType{methods}
+\name{normalize,metabarcoding.data-method}
+\alias{normalize,metabarcoding.data-method}
+\alias{normalize-methods,metabarcoding.data}
+\title{Normalizes read counts by sample or by MOTU.}
+\usage{
+\S4method{normalize}{metabarcoding.data}(data, MARGIN = "sample",
+  as.matrix = FALSE)
+}
+\arguments{
+\item{data}{The \code{\linkS4class{metabarcoding.data}} instance
+on normalisation have to be computed.}
+
+\item{MARGIN}{Indicates if the sums have to be computed across 
+samples or motus. 
+Allowed values are :
+\itemize{
+  \item{'sample' or 1} for computing sum across samples
+  \item{'motu' or 2} for computing sum across motus
+  }}
+
+\item{as.matrix}{Logical indicating if the normalized aboundancies
+must be returned as a simple \code{matrix} (TRUE) or as a new
+instance of the \code{\linkS4class{metabarcoding.data}} class
+(FALSE, the default case).}
+}
+\value{
+Returns a new instance of \code{\linkS4class{metabarcoding.data}}
+        or a \code{numeric} matrix according to the \code{return.as.matrix}
+        parameter.
+}
+\description{
+Method \code{normalize} computes a normalized read aboundancy matrix
+(relative frequency matrix) of a \code{\link{metabarcoding.data}} instance.
+Normalization can be done according aboundancies per sample or per MOTU.
+}
+\examples{
+# load termite data set from the ROBITools sample data
+data(termes)
+
+# Computes normalized aboundancies per sample
+termes.norm = normalize(termes,MARGIN="sample")
+
+# Computes normalized aboundancies per sample and
+# stores the result as a new layer into the thermes
+# structure
+termes$normalized = normalize(termes,MARGIN="sample",as.matrix=TRUE)
+
+}
+\seealso{
+\code{\linkS4class{metabarcoding.data}}
+}
+\author{
+Aurelie Bonin
+}