Commit the man pages and make aggregate public again

2018-07-25 21:38:48 +02:00
parent 51f152cca4
commit 052d6edc75
41 changed files with 1659 additions and 5 deletions
--- a/man/metabarcoding-data-class.Rd
+++ b/man/metabarcoding-data-class.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/02_class_metabarcoding.data.R
+\docType{class}
+\name{metabarcoding.data}
+\alias{metabarcoding.data}
+\title{DNA metabarcoding experiment description class}
+\description{
+A S4 class describing a DNA metabarcoding experiment. It groups
+three data frames describing samples, motus and occurrences of 
+MOTUs per sample
+}
+\section{Slots}{
+ 
+ \describe{
+   \item{\code{reads}:}{Matrix of class \code{"numeric"},  
+                        containing the counts of reads per samples
+                        \itemize{
+                          \item{1 samples per line}
+                          \item{1 sequence per column}
+                        }
+                       }
+                       
+   \item{\code{samples}:}{Object of class \code{"data.frame"}, describing samples
+                        \itemize{
+                          \item{1 samples per line}
+                          \item{1 property per column}
+                        }
+                      }
+                      
+   \item{\code{motus}:}{Object of class \code{"data.frame"}, describing MOTUs (sequences)
+                        \itemize{
+                          \item{1 MOTU per line}
+                          \item{1 property per column}
+                        }
+                      }
+                      
+   \item{\code{layers}:}{Object of class \code{"list"}, containing a set of data layers 
+                         linking motus and samples. Each element of the list is a matrix
+                         of the same size than the \code{read} slot with
+                        \itemize{
+                          \item{1 samples per line}
+                          \item{1 sequence per column}
+                        }
+                      }
+       
+   \item{\code{scount}:}{Object of class \code{"integer"}, containing the count of sample}             
+       
+   \item{\code{mcount}:}{Object of class \code{"integer"}, containing the count of MOTUs}             
+       
+   \item{\code{sample.margin}:}{Vector of class \code{"numeric"},  describing the total count of 
+                         sequence per sample. By default this slot is set by applying sum
+                        to the reads data.frame lines}             
+
+   \item{\code{taxonomy}:}{Object of class \code{"taxonomy.obitools"}, linking the DNA metabarcoding
+                           experiment to a taxonomy}             
+       
+   \item{\code{taxid}:}{Vector of class \code{"character"}, list of MOTUs' attributes to manage as taxid}             
+ }
+}
+
+\seealso{
+\code{\link{taxonomy.obitools}},
+}
+\author{
+Eric Coissac
+}
+\keyword{DNA}
+\keyword{metabarcoding}