69 lines
2.6 KiB
R
69 lines
2.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/02_class_metabarcoding.data.R
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\docType{class}
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\name{metabarcoding.data}
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\alias{metabarcoding.data}
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\title{DNA metabarcoding experiment description class}
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\description{
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A S4 class describing a DNA metabarcoding experiment. It groups
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three data frames describing samples, motus and occurrences of
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MOTUs per sample
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}
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\section{Slots}{
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\describe{
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\item{\code{reads}:}{Matrix of class \code{"numeric"},
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containing the counts of reads per samples
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\itemize{
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\item{1 samples per line}
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\item{1 sequence per column}
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}
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}
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\item{\code{samples}:}{Object of class \code{"data.frame"}, describing samples
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\itemize{
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\item{1 samples per line}
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\item{1 property per column}
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}
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}
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\item{\code{motus}:}{Object of class \code{"data.frame"}, describing MOTUs (sequences)
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\itemize{
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\item{1 MOTU per line}
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\item{1 property per column}
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}
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}
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\item{\code{layers}:}{Object of class \code{"list"}, containing a set of data layers
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linking motus and samples. Each element of the list is a matrix
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of the same size than the \code{read} slot with
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\itemize{
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\item{1 samples per line}
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\item{1 sequence per column}
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}
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}
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\item{\code{scount}:}{Object of class \code{"integer"}, containing the count of sample}
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\item{\code{mcount}:}{Object of class \code{"integer"}, containing the count of MOTUs}
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\item{\code{sample.margin}:}{Vector of class \code{"numeric"}, describing the total count of
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sequence per sample. By default this slot is set by applying sum
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to the reads data.frame lines}
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\item{\code{taxonomy}:}{Object of class \code{"taxonomy.obitools"}, linking the DNA metabarcoding
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experiment to a taxonomy}
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\item{\code{taxid}:}{Vector of class \code{"character"}, list of MOTUs' attributes to manage as taxid}
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}
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}
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\seealso{
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\code{\link{taxonomy.obitools}},
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}
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\author{
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Eric Coissac
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}
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\keyword{DNA}
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\keyword{metabarcoding}
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