BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data


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Documentation for package ‘BioMM’ version 1.0.0

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baseGLMnet Prediction by generalized linear regression models
baseModel Base supervised machine learning models for prediction
baseRandForest Prediction by random forest
baseSVM Prediction by SVM
BioMM BioMM end-to-end prediction
BioMMreconData Reconstruct stage-2 data by supervised machine learning prediction
BioMMstage1pca Reconstruct stage-2 data by PCA
BioMMstage2pred Prediction performance for stage-2 data using supervised machine learning
classifiACC Compute the classification accuracy
getDataAfterFS Return the data after feature selection
getMetrics Compute the evaluation metrics
omics2chrlist Map individual probes into chromosome
omics2genelist Map individual probes into gene
omics2pathlist Map individual probes into pathway
plotRankedFeature Plot top outcome-associated features
plotVarExplained Plot data summary statistics
predByBS Bootstrap resampling prediction via supervised machine learning with feature selection
predByCV Cross validation prediction by supervised machine learning and feature selection
predByFS Prediction by supervised machine learning along with feature selection