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Analyzing High-Dimensional Gene Expression and DNA Methylation Data with R

PIPELINES TO ANALYZE “OMICS” DATARNA-Seq GENE EXPRESSION IN S2-DRSC CELLSMICROARRAY GENE EXPRESSION IN YEAST CELLS AND IN PROSTATE SAMPLESDNA METHYLATION IN NORMAL AND COLON/RECTAL ADENOCARCINOMA SAMPLESMICROARRAY GENE EXPRESSION DATAData generationPreprocessing and quality control of microarray dataDATA FROM NEXT GENERATION SEQUENCINGData generationPreprocessing and quality control of bulk RNA-Seq data: Genome-scale epigenetic dataDATA GENERATIONQUALITY CONTROL AND PREPROCESSING OF DNA METHYLATION DATAThe control probe adjustment and reduction of global correlation pipeline (CPACOR)Quantile normalization with ComBatCELL TYPE COMPOSITION INFERENCESReference-based methodsReference-free methodsAPPENDIX – MODIFIED PROGRAMS IN THE CPACOR WITH AN APPLICATION: Screening genome-scale genetic and epigenetic dataSCREENING VIA TRAINING AND TESTING SAMPLESSCREENING INCORPORATING SURROGATE VARIABLESSURE INDEPENDENCE SCREENINGCorrelation learningNON- AND SEMI-PARAMETRIC SCREENING TECHNIQUESRandom forestSupport vector machine: Cluster Analysis in Data miningNON-PARAMETRIC CLUSTER ANALYSIS METHODSDistancesPartitioning-based methodsHierarchical clusteringHybrids of partitioning-based and hierarchical clusteringExamples – clustering to detect gene expression patternsCLUSTER ANALYSES IN LINEAR REGRESSIONSBICLUSTER ANALYSESJOINT CLUSTER ANALYSIS: Methods to select genetic and epigenetic factors based on linear associationsFREQUENTIST APPROACHESElastic netAdaptive LASSOSmoothly clipped absolute deviation (SCAD)BAYESIAN APPROACHESZellner’s g-priorExtension of Zellner’s g-prior to multi-components G-priorThe spike-and-slab priorEXAMPLES – SELECTING IMPORTANT EPIGENETIC FACTORS: Non- and semi-parametric methods to select genetic and epigenetic factorsVARIABLE SELECTION BASED ON SPLINESOVERVIEW OF THE ANOVA-BASED APPROACHVARIABLE SELECTION BUILT UPON REPRODUCING KERNELSEXAMPLESSelecting important epigenetic factorsSelecting variables with known underlying truth: Network construction and analysesUNDIRECTED NETWORKSThe two-stage graphs selection methodThe GGMselect package and gene expression examplesCORRELATION NETWORKSBAYESIAN NETWORKSNETWORK COMPARISONSComparing undirected networksComparing Bayesian networksBibliography

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