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

Documentation for package ‘BioMM’ version 1.8.0

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
BioMMstage2pred	Prediction performance for stage-2 data using supervised machine learning
cirPlot4pathway	Circular plot for a set of pathways
classifiACC	Compute the classification accuracy
getDataByFilter	Return the data by feature filtering
getMetrics	Compute the machine learning evaluation metrics
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
reconBySupervised	Reconstruct stage-2 data by supervised machine learning prediction
reconByUnsupervised	Reconstruct stage-2 data by PCA