HowToRoxygen2

## FUNCTIONS
#' A title
#' 
#' A description
#' 
#' @param param1 A \code{class}. A description of the parameter,
#' its use, the values it can take.
#' @param param2 ...
#' @param param3 ...
#'
#' @details
#' Details regarding the arguments of the function, the requirements
#' for this function to work (required columns in input files, 
#' architecture offile tree..).
#'
#' @return A \code{class} with a descritpion of what it contains
#' depending on the input parameters.
#'
#' @author Author One, Author Two
#'
#' @seealso \code{\link{anotherFunction}}, \code{\link{aClass}},
#' \code{link{aMethod}}
#'
#' @examples
#' #A first example
#' res <- thefunction(param1 = 12, param2 = NULL, param3 = "FDR")
#'
#' #A second example
#' res2 <- thefunction(param1 = 12, param2 = NULL, param3 = "absolute")
#'
#' @export
#' @importFrom package1 function1 function2
#' @importClassesFrom package1 class1

To have multiple functions in the same file:
 Document the first function as described above + add @param for the parameters
 of the second function + specify @rdname filename.
 In the second function:
	#' @rdname filename
	#' @export
 usage section gets created autiomatically for both functions in the same file.


## CLASSES
#' classname class
#' 
#' Description of the class, its purpose
#' 
#' @section Slots:
#' \describe{
#'  \item{featureRange}{A \code{RangedData object}. The ranges and sequences of 
#' the peptides and their associated annotation.}
#'  \item{phenoData}{An \code{AnnotatedDataFrame}. Annotation for the samples.}
#'  \item{assayData}{}
#'  \item{featureData}{}
#'  \item{annotation}{}
#'  \item{protocolData}{Slots inherited from \code{ExpressionSet}.}
#' }
#'
#' @details
#' See \code{?`peptideSet-methods`} for a list of accessors and method associated
#' with the class.
#'
#' @seealso \code{\link{ExpressionSet}}, \code{\link{peptideSet-methods}}
#'
#' @importClassesFrom Biobase ExpressionSet
#' @importClassesFrom IRanges RangedData
#' @aliases -class
#' @exportClass peptideSet
#' @author First Last 
#'