├── DESCRIPTION ├── IMAGES ├── Example DBAnnotate process.png ├── Example.Hierarchical.clustering.results.PNG ├── Example.MS.MS.match.results.PNG ├── M237T212.Y_variable_4.png ├── M237T212.Y_variable_4_BOXPLOT.png ├── M759T55 .png ├── M759T55 CORR .png ├── MSConvert_settings_MS1.PNG ├── MSConvert_settings_MS2.PNG ├── MS_MS_example.png ├── PCA_scores_model_1.png ├── PCA_scores_model_2.png ├── Sum_reprod_feat_example.PNG ├── X_X_heatmap.PNG ├── X_Y_heatmap.PNG ├── suggested_subdirectory_structure_A.png └── suggested_subdirectory_structure_B.png ├── LICENSE ├── NAMESPACE ├── R ├── batchAdj.R ├── blankSub.R ├── coVarTypeStat.R ├── cvCalc.R ├── cytoScapeMap.R ├── example_Exp_MS1features.R ├── hotEllipse.R ├── lmResDiff.R ├── loessFitKfoldCV.R ├── loessSmooth.R ├── loessWrapperMod.R ├── logTrans.R ├── manhattanPlot.R ├── pcaClustId.R ├── pcaOutId.R ├── pcaResOut.R ├── plotPcsEx.R ├── preProc.R ├── ramClustMod.R ├── rtCorrClust.R ├── signNorm.R ├── tableCheckRead.R ├── targMS2csv.R ├── volcanoPlot.R └── zeroFill.R ├── README.md ├── README.txt ├── inst ├── doc │ ├── MetMSLine.pdf │ └── MetMSLineBasics.pdf └── extdata │ ├── MS1features_example.csv │ ├── coVariates.csv │ ├── synthetic_MS_data.csv │ └── synthetic_coVar_data.csv ├── man ├── batchAdj.Rd ├── blankSub.Rd ├── coVarTypeStat.Rd ├── cvCalc.Rd ├── cytoScapeMap.Rd ├── example_Exp_MS1features.Rd ├── hotEllipse.Rd ├── lmResDiff.Rd ├── loessFitKfoldCV.Rd ├── loessSmooth.Rd ├── loessWrapperMod.Rd ├── logTrans.Rd ├── manhattanPlot.Rd ├── pcaClustId.Rd ├── pcaOutId.Rd ├── pcaResOut.Rd ├── plotPcsEx.Rd ├── preProc.Rd ├── ramClustMod.Rd ├── rtCorrClust.Rd ├── signNorm.Rd ├── tableCheckRead.Rd ├── targMS2csv.Rd ├── volcanoPlot.Rd └── zeroFill.Rd └── vignettes ├── MetMSLine.R ├── MetMSLine.Rmd ├── MetMSLine.html ├── MetMSLine.pdf ├── MetMSLineBasics.R ├── MetMSLineBasics.Rmd ├── MetMSLineBasics.html └── MetMSLineBasics.pdf /DESCRIPTION: -------------------------------------------------------------------------------- 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