R/MSstatsPTM.R

In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications

#' MSstatsPTM: A package for detecting differentially abundant 
#' post-translational modifications (PTM) in mass spectrometry-based 
#' proteomic experiments.
#'
#' A set of tools for detecting differentially abundant PTMs and proteins in
#' shotgun mass spectrometry-based proteomic experiments. The package can handle
#' a variety of acquisition types, including label free and TMT experiments, 
#' acquired with DDA, DIA, SRM or PRM acquisition methods. The 
#' package includes tools to convert raw data from different spectral processing
#' tools, summarize feature intensities, and fit a linear mixed effects model. A
#' major advantage of the package is to leverage a separate global profiling run
#' and adjust the PTM fold change for changes in the unmodified protein, showing
#' the unconvoluted PTM fold change. Finally, the package includes functionality
#' to plot a variety of data visualizations.
#'
#' @section functions :
#' \itemize{
#'   \item \code{\link{FragPipetoMSstatsPTMFormat}} : Generates MSstatsPTM 
#'   required input format for TMT FragePipe outputs.
#'   \item \code{\link{MaxQtoMSstatsPTMFormat}} : Generates MSstatsPTM required
#'   input format for label-free and TMT MaxQuant outputs.
#'   \item \code{\link{ProgenesistoMSstatsPTMFormat}} : Generates MSstatsPTM 
#'   required input format for label-free Progenesis outputs.
#'   \item \code{\link{SpectronauttoMSstatsPTMFormat}} : Generates MSstatsPTM 
#'   required input format for label-free Spectronaut outputs.
#'   \item \code{\link{SkylinetoMSstatsPTMFormat}} : Generates 
#'   MSstatsPTM required input format for Skyline outputs.
#'   \item \code{\link{PStoMSstatsPTMFormat}} : Generates 
#'   MSstatsPTM required input format for PEAKS outputs.
#'   \item \code{\link{PDtoMSstatsPTMFormat}} : Generates 
#'   MSstatsPTM required input format for Proteome Discoverer outputs.
#'   \item \code{\link{dataSummarizationPTM}} : Summarizes PSM level 
#'   quantification to peptide (modification) and protein level quantification.
#'   For use in label-free analysis
#'   \item \code{\link{dataSummarizationPTM_TMT}} : Summarizes PSM level 
#'   quantification to peptide (modification) and protein level quantification.
#'   For use in TMT analysis.
#'   \item \code{\link{dataProcessPlotsPTM}} : Visualization for explanatory
#'   data analysis. Specifically gives ability to plot Profile and Quality 
#'   Control plots.
#'   \item \code{\link{groupComparisonPTM}} : Tests for significant changes in 
#'   PTM and protein abundance across conditions. Adjusts PTM fold change for 
#'   changes in protein abundance.
#'   \item \code{\link{groupComparisonPlotsPTM}} : Visualization for model-based
#'    analysis and summarization
#' }
#'
#' @docType _PACKAGE
#' @name MSstatsPTM
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