# Scoring Personalized Molecular Portraits

## Documentation for package ‘pathMED’ version 1.3.0

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

## Help Pages

ann2term | Annotate the pathways from a scores matrix
buildRefObject | Create a reference data object for input to the pathMED functions
dissectDB | Split pathways into coexpressed subpathways
genesetsData | Preloaded gene sets
getScores | Calculate pathways scores for a dataset
methodsML | Prepare the models parameter for the trainModel function
mScores_createReference | Create a reference dataset based on M-scores
mScores_filterPaths | Filter pathways from the reference M-scores dataset
mScores_imputeFromReference | Estimate M-scores for a dataset without healthy controls
pathMEDExampleData | Example of test gene expression data
pathMEDExampleMetadata | Metadata of test gene expression data
predictExternal | Predict conditions in external datasets
refData | Example of reference gene expression datasets
trainModel | Train ML models and perform internal validation