# Biologically Explainable Machine Learning Framework

## Documentation for package ‘BioM2’ version 1.1.3

- DESCRIPTION file.
- Package NEWS.

## Help Pages

AddUnmapped | Add unmapped probe
baseModel | Prediction by Machine Learning
BioM2 | Biologically Explainable Machine Learning Framework
FindParaModule | Find suitable parameters for partitioning pathways modules
GO2ALLEGS_BP | An example about pathlistDB
GO_Ancestor | Pathways in the GO database and their Ancestor
GO_Ancestor_exact | Pathways in the GO database and their Ancestor
HyBioM2 | BioM2 Hyperparametric Combination
MethylAnno | An example about FeatureAnno for methylation data
MethylData_Test | An example about TrainData/TestData for methylation data
PathwaysModule | Delineate differential pathway modules with high biological interpretability
PlotCorModule | Correlalogram for Biological Differences Modules
PlotPathFearture | Visualisation of significant pathway-level features
PlotPathInner | Visualisation Original features that make up the pathway
PlotPathNet | Network diagram of pathways-level features
ShowModule | Display biological information within each pathway module
Stage1_FeartureSelection | Stage 1 Fearture Selection
Stage2_FeartureSelection | Stage 2 Fearture Selection
TransAnno | An example about FeatureAnno for gene expression
TransData_Test | An example about TrainData/TestData for gene expression
VisMultiModule | Visualisation of the results of the analysis of the pathway modules