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

## Documentation for package ‘DaMiRseq’ version 2.2.0

- 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