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

## Documentation for package ‘BioMM’ version 1.3.0

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

## Help Pages

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 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