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

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Documentation for package ‘DaMiRseq’ version 2.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.EnsembleLearningNcl	Build a Multi-Class Classifier using 'Staking' Learning strategy.
DaMiR.EnsL_Predict	Predict new samples class
DaMiR.EnsL_Test	Test Binary Classifiers
DaMiR.EnsL_Train	Train a Binary 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.iTSadjust	Batch correction of normalized Independent Test Set
DaMiR.iTSnorm	Normalization of Independent Test Set
DaMiR.makeSE	Import RNA-Seq count data and variables
DaMiR.MDSplot	Plot multidimentional scaling (MDS)
DaMiR.ModelSelect	Select the best classification model
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