Scoring Personalized Molecular Portraits


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Documentation for package ‘pathMED’ version 1.0.0

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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