################################################################################
#' @title Deprecated S4 class to store experiment data for proteomics experiment
#' This is a S4 class inherits from the virtual class
#' \code{\link{ExperimentData-class}}. The purpose of this class is to store
#' all the additional experiment information from a proteomics experiment.
#' This class has a list like structure. It contains five slots and each is
#' either a character or numeric value.
#' @slot institute The institute or lab where the experiment was conducted.
#' @exportClass ProteomicsExperimentData
setClass(
Class = "ProteomicsExperimentData",
representation = representation(
institute = "characterOrNULL"
),
contain = "ExperimentData",
prototype = prototype(
institute = NULL
)
)
################################################################################
# setClassUnion("ProteomicsExperimentDataOrNULL",
# c("ProteomicsExperimentData", "NULL"))
################################################################################
#' @title Deprecated Construction method for the S4 class ProteomicsExperimentData
#' @description The construction method to build a
#' \code{\link{ProteomicsExperimentData-class}} object.
#' @param institute Character indicating the institute or lab where the experiment was conducted.
#' @export
ProteomicsExperimentData = function(
institute = NULL
){
new("ProteomicsExperimentData",
institute = institute)
}
################################################################################
#' @name ProteomicsSet-class
#' @title S4 class to store proteomics experiment data
#'
#' @description
#' This is a S4 class inherits from the virtual
#' \code{\link{mSet-class}} to store the proteomics data. This class acts
#' as a data container for the proteomics data. Once data is cleaned and
#' passed into the class, it is ready to do statistical analysis and
#' visualization.
#'
#' @slot conc_table A \code{\link{conc_table-class}} object that stores the
#' concentration information from the experiment. The column names should be
#' the feature IDs, and the rownames should be the row IDs. This should be a
#' numeric matrix.
#'
#' @slot sample_table A \code{\link{sample_table-class}} object that stores the
#' sample meta-data information. The row names should be sample IDs and
#' should match the column names of the conc_table.
#'
#' @slot feature_data A \code{\link{feature_data-class}} object that stores the
#' feature infromation during the experiment. The row names should be feature
#' IDs and should match the row names of the conc_table.
#'
#' @slot experiment_data A list contains additional experiment information.
#'
#' @exportClass ProteomicsSet
#' @author Chenghao Zhu
setClass(Class = "ProteomicsSet", contains = "mSet")
################################################################################
#' @name ProteomicsSet
#' @title Construct a ProteomicsSet object
#' @description This is the method to construct a
#' \code{\link{ProteomicsSet-class}} object.
#'
#' @param conc_table A \code{\link{conc_table-class}} object that stores the
#' concentration information from the experiment. The column names should be
#' the feature IDs, and the rownames should be the row IDs. This should be a
#' numeric matrix.
#'
#' @param sample_table A \code{\link{sample_table-class}} object that stores the
#' sample meta-data information. The row names should be sample IDs and
#' should match the column names of the conc_table.
#'
#' @param feature_data A \code{\link{feature_data-class}} object that stores the
#' feature infromation during the experiment. The row names should be feature
#' IDs and should match the row names of the conc_table.
#'
#' @param experiment_data A list contains additional experiment information.
#'
#' @export
#' @author Chenghao Zhu
#' @export
ProteomicsSet = function(
conc_table = NULL,
sample_table = NULL,
feature_data = NULL,
experiment_data = NULL
){
new("ProteomicsSet",
conc_table = conc_table,
sample_table = sample_table,
feature_data = feature_data,
experiment_data = experiment_data)
}
################################################################################
#' @export
setMethod(
"show", signature = "ProteomicsSet",
definition = function(object){
cat(str_pad(">>>>>> Proteomics Experiment <<<<<<", 54, "left", " "))
cat("\n")
callNextMethod()
}
)
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