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#'Extracts the quality control samples of an AFLP object
#'
#'@param data An AFLP object
#'@param which Which quality information to extract. Must be one of c("all",
#'"specimen", "replicate"). Defaults to "all".
#'@return In case when which == "all" a list with 2 data.frames containing the
#'quality control samples. Otherwise a data.frame with the selected quality
#'control samples.
#'@author Thierry Onkelinx \email{Thierry.Onkelinx@@inbo.be}, Paul Quataert
#'@seealso \code{\link{QC-method}}
#'@keywords attribute
#'@examples
#'
#' data(Tilia)
#' QC(Tilia)
#'
#'@exportMethod QC
setGeneric("QC", function(data, which = c("all", "specimen", "replicate")) {
standardGeneric("QC")
})
#'Extracts the quality control samples of an AFLP object
#'
#'
#'@name QC-method
#'@aliases QC-method QC,AFLP-method
#'@docType methods
#'@section Methods: \describe{
#'
#'\item{x = "AFLP"}{Returns the QC information from an AFLP object}
#'}
#'@keywords methods attribute
#'@export
setMethod("QC", signature(data = "AFLP"), function(data, which = c("all", "specimen", "replicate")) {
which <- match.arg(which)
if(which == "all"){
return(data@QC)
} else if(which == "specimen"){
return(data@QC[["Specimen"]])
} else {
return(data@QC[["Replicate"]])
}
})
#'Adds or overwrites quality control samples
#'
#'Adds or overwrites quality control samples in an AFLP object.
#'
#'
#'@name QC<--methods
#'@aliases QC<--methods QC<-,AFLP-method
#'@docType methods
#'@section Methods: \describe{
#'
#'\item{data = "AFLP"}{\code{data} is updated with the new quality control
#'samples} }
#'@keywords methods
#'@exportMethod QC<-
setGeneric("QC<-", function(data, which, value){
standardGeneric("QC<-")
})
#'Adds or overwrites quality control samples in an AFLP object.
#'
#'
#'@param data An AFLP object
#'@param value When which == "all", value must be a list with quality
#'information. Otherwise a data.frame with the corresponding quality
#'information.
#'@param which A character value matching c("all", "specimen", "replicate").
#'Defaults to "all".
#'@return \code{data} is updated with the new quality information
#'@author Thierry Onkelinx \email{Thierry.Onkelinx@@inbo.be}, Paul Quataert
#'@seealso \code{\link{QC}}
#'@keywords manip
#'@examples
#'
#' data(Tilia)
#' tmp <- replicates(Tilia)
#' QC(Tilia, which = "all") <- list(
#' Specimen = data.frame(
#' Specimen = tmp$Specimen[grep("QC", tmp$Specimen)],
#' Type = "method"
#' ),
#' Replicate = data.frame(
#' Replicate = tmp$Replicate[grep("qc", tmp$Replicate)],
#' Type = "method"
#' )
#' )
#' QC(Tilia, which = "specimen") <- data.frame(
#' Specimen = tmp$Specimen[grep("QC", tmp$Specimen)],
#' Type = "method"
#' )
#' QC(Tilia, which = "replicate") <- data.frame(
#' Replicate = tmp$Replicate[grep("qc", tmp$Replicate)],
#' Type = "method"
#' )
#'
setMethod("QC<-", signature(data = "AFLP"), function(data, which = c("all", "specimen", "replicate"), value){
which <- match.arg(which)
if(which == "all"){
data@QC <- value
} else if(which == "specimen"){
data@QC[["Specimen"]] <- value
} else {
data@QC[["Replicate"]] <- value
}
return(data)
})
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