Data Mining for RNA-seq data: normalization, feature selection and classification


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Documentation for package ‘DaMiRseq’ version 1.8.0

Help Pages

DaMiR.Allplot Quality assessment and visualization of expression data
DaMiR.Clustplot Expression data clustering and heatmap
DaMiR.corrplot Correlation Plot
DaMiR.EnsembleLearning Build Classifier using 'Staking' Ensemble Learning strategy.
DaMiR.EnsembleLearning2cl Build a Binary Classifier using 'Staking' Learning strategy.
DaMiR.EnsembleLearning2cl_Predict Predict new samples class
DaMiR.EnsembleLearning2cl_Test Test Binary Classifiers
DaMiR.EnsembleLearning2cl_Training Train a Binary Classifier using 'Staking' Learning strategy.
DaMiR.EnsembleLearningNcl Build a Multi-Class Classifier using 'Staking' Learning strategy.
DaMiR.FBest Select best predictors to build Classification Model
DaMiR.FReduct Remove highly correlated features, based on feature-per-feature correlation.
DaMiR.FSelect Feature selection for classification
DaMiR.FSort Order features by importance, using RReliefF filter
DaMiR.goldenDice Generate a Number to Set Seed
DaMiR.makeSE Import RNA-Seq count data and variables
DaMiR.MDSplot Plot multidimentional scaling (MDS)
DaMiR.normalization Filter non Expressed and 'Hypervariant' features and Data Normalization
DaMiR.sampleFilt Filter Samples by Mean Correlation Distance Metric
DaMiR.SV Identification of Surrogate Variables
DaMiR.SVadjust Remove variable effects from expression data
DaMiR.transpose Matrix transposition and replacement of '.' and '-' special characters
data_min Example gene-expression dataset for DaMiRseq package
data_norm A dataset with a normalized matrix to test several DaMiRseq functions: sample data are a subset of Genotype-Tissue Expression (GTEx) RNA-Seq database (dbGap Study Accession: phs000424.v6.p1)
data_reduced Example gene-expression dataset for DaMiRseq package
data_relief Example ranking dataset for DaMiRseq package
df Example gene-expression dataset for DaMiRseq package
SE Example gene-expression dataset for DaMiRseq package
selected_features Example gene-expression dataset for DaMiRseq package
SEtest_norm A sample dataset with a normalized count matrix for "testthat" functions.
sv Example Surrogate Variables dataset for DaMiRseq package