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

Documentation for package ‘BioMM’ version 1.0.0

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