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 dataGenome-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 APPLICATIONScreening genome-scale genetic and epigenetic dataSCREENING VIA TRAINING AND TESTING SAMPLESSCREENING INCORPORATING SURROGATE VARIABLESSURE INDEPENDENCE SCREENINGCorrelation learningNON- AND SEMI-PARAMETRIC SCREENING TECHNIQUESRandom forestSupport vector machineCluster 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 ANALYSISMethods 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 FACTORSNon- 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 truthNetwork 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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