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#' @name MSstats_data
#' @docType data
#' @title Testing dataset in MSstats format.
#' @description A small table with the column names corresponding to the MSstats format.
#' This data is intended only to test functions.
#' @author Peter Blattmann
NULL
#' @name OpenSWATH_data
#' @aliases data
#' @docType data
#' @title Testing dataset from OpenSWATH.
#' @description A small selection of the data obtained from the iPortal pipeline for an
#' SWATH/DIA experiment with perturbations relating to cholesterol regulation.
#' Protein and Peptides have been anonymized as the data is unpublished.
#' The FDR version of the test data contains modified (lowered) decoy peak
#' group m_scores to simulate FDR behaviour of a large dataset.
#' @author Peter Blattmann
NULL
#' @name Spyogenes
#' @docType data
#' @title S.pyogenes example data.
#'
#' @description A table containing SWATH-MS data from S.pyogenes.
#' This table was generated from the original data deposited on PeptideAtlas
#' (PASS00289, file "rawOpenSwathResults_1pcnt_only.tsv") by selecting only
#' the column necessary for the SWATH2stats.
#'
#' @references Rost, H. L., et al. (2014). OpenSWATH enables automated,
#' targeted analysis of data-independent acquisition MS data.
#' Nat Biotechnol 32(3): 219-223.
NULL
#' @name Study_design
#' @docType data
#' @title A table containing the meta-data defining the study design of the OpenSWATH data.
#'
#' @description This table contains a unique identifier in the column "Filename"
#' corresponding to the filename in the SWATH data.
#' In the column "Condition" the perturbation performed is described.
#' In the column "BioReplicate" the biological replicate is indicated.
#' In the column "Run" a unique identifier for each injection.
#' Technical injections would have different Run numbers but the same
#' BioReplicate number.
#'
#' @author Peter Blattmann
NULL
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