R/MSstatsTMTPTM.R

In MSstatsTMTPTM: Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

#' MSstatsTMTPTM: A package for detecting differencially abundant post
#' translational modifications (PTM) in shotgun mass spectrometry-bsed proteomic
#'  experiments with tandem mass tag (TMT) labeling.
#'
#' A set of tools for detecting differentially abundant PTMs and proteins in
#' shotgun mass spectrometry-based proteomic experiments with tandem mass tag
#' (TMT) labeling. The functions in this package should be used after
#' PTM/protein summarization. They can be used to both plot the summarized
#' results and model the summarized datasets.
#'
#' @section functions :
#' \itemize{
#'   \item \code{\link{dataProcessPlotsTMTPTM}} : Data visualization of PTM and
#'   global protein levels. Can plot either Profile plots to identify the
#'   potential sources of variation for each protein, or quality control
#'   plots to evaluate the systematic bias between MS runs.
#'   \item \code{\link{groupComparisonTMTPTM}} : Tests for significant changes
#'   in PTM abundance adjusted for global protein abundance across conditions
#'   based on a family of linear mixed-effects models in TMT experiment.
#' }
#'
#' @docType package
#' @name MSstatsTMTPTM
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