exportPattern("^[[:alpha:]]+")

import(MSnbase)
import(DAPARdata)
import(RColorBrewer)
import(Cairo)
import(png)
import(lattice)
import(reshape2)
import(tmvtnorm)
import(ggplot2)
import(norm)
import(highcharter)
import(vioplot)
import(impute)
import(knitr)
importFrom("doParallel", "registerDoParallel")
importFrom("dplyr", "left_join", "mutate","tbl_df", "select_","data_frame", "last")
importFrom("tidyr", "gather")
importFrom("foreach", "foreach", "%dopar%")
importFrom("AnnotationDbi", "keys")
importFrom("parallel", "detectCores")
import("Matrix")
import(cp4p)

import(tidyverse)
import(imp4p)
importFrom("graphics", "par", "boxplot", "axis", "mtext", "abline", "points", 
            "legend", "lines",  "barplot", "text",
           "layout", "plot.new", "strheight", "strwidth", "title","plot.window")
 
importFrom("stats", "lowess", "cor", "density","pexp", "mad", 
            "var", "t.test", "dist", "hclust", "setNames", 
            "median", "p.adjust", "model.matrix", "rnorm","na.omit",
           "quantile", "rbeta", "runif", "sd", "pchisq", "residuals","formula", "lm", "logLik")
importFrom("preprocessCore", "normalize.quantiles")
importFrom("gplots", "heatmap.2")
import("limma")
importFrom("pcaMethods", "completeObs", "pca")
importFrom("scales", "alpha")
importFrom("grDevices", "colorRampPalette", "palette", "heat.colors")
importFrom("utils", "read.csv", "read.table", "de", "str","write.csv", "zip")
importFrom("lme4", "getME")
importFrom("openxlsx", "getSheetNames", "createWorkbook", "addWorksheet", "writeData", "saveWorkbook")
import("readxl")
import("siggenes") # SAM
import("graph")
importFrom("stringr", "str_match_all")
importFrom("clusterProfiler", "bitr", "enrichGO", "groupGO")
import("imputeLCMD")

export(
"writeMSnsetToExcel",
"writeMSnsetToCSV",
"createMSnset",
"readExcel",
"listSheets",
"addOriginOfValue","saveParameters",
"buildLogText",
"rbindMSnset"

,"wrapper.boxPlotD","boxPlotD"
,"wrapper.densityPlotD","densityPlotD"
,"wrapper.CVDistD","CVDistD"
,"wrapper.corrMatrixD","corrMatrixD"
,"wrapper.heatmapD","heatmapD"
,"wrapper.mvPerLinesHisto", "mvPerLinesHisto"
,"wrapper.mvPerLinesHisto_HC", "mvPerLinesHisto_HC"
,"wrapper.mvPerLinesHistoPerCondition", "mvPerLinesHistoPerCondition"
,"wrapper.mvHisto", "mvHisto"


,"wrapper.mvTypePlot","mvTypePlot"
,"wrapper.mvImage","mvImage"
,"heatmap.DAPAR"

,"mvFilter"
,"mvFilterFromIndices"
,"mvFilterGetIndices"
,"removeLines"
,"deleteLinesFromIndices"
,"StringBasedFiltering"
,"getIndicesOfLinesToRemove"
,"wrapper.normalizeD","normalizeD"
,"wrapper.compareNormalizationD","compareNormalizationD"
,"getListNbValuesInLines"

,"reIntroduceMEC"
,"findMECBlock"
,"wrapper.impute.fixedValue"
,"wrapper.impute.detQuant"
,"wrapper.impute.slsa"
,"getQuantile4Imp"


,"pepAgregate"
,"BuildAdjacencyMatrix"
,"GraphPepProt"
,"BuildColumnToProteinDataset"
,"BuildColumnToProteinDataset_par"
,"getProteinsStats"



## limma Complete test
,"limmaCompleteTest"
,"check.design"
,"check.conditions"




,"wrapper.t_test_Complete"
,"diffAnaVolcanoplot_rCharts"
,"diffAnaSave"
,"diffAnaComputeFDR"
,"wrapperCalibrationPlot"
,"hc_FC_DensityPlot"


,"getProcessingInfo"

,"pepa.test"



,"group_GO"
,"enrich_GO"
,"univ_AnnotDbPkg"
,"GOAnalysisSave"
,"scatterplotEnrichGO_HC"
,"barplotEnrichGO_HC"
,"barplotGroupGO_HC"

,"my_hc_ExportMenu"


)
