Man pages for olivmrtn/MachineLearningGWAS
Machine Learning for Genome Wide Association Studies
| aggregateMDT | Aggregate FeatureIDs Into Higher Level IDs |
| annotateMDT | Annotate MDT Objects |
| asMatrixMDT | Convert mtable data.table to matrix |
| chrAsCharacter | Chromsome integer values as character |
| chrAsNumeric | Chromsome character values as integer |
| fillMDT | Fill missing values for MDT objects. |
| filterMDT | Filter MDT Objects |
| importPhenotype | Adds phenotype data to MDT object |
| manhattanPlot | Manhattan Plot for MDT and MLGWAS objects. |
| MDT-class | Mutation Data Table |
| mdtToGRanges | Convert MDT to Genomic Ranges |
| MLGWAS-class | Machine Learning for Genome Wide Association Studies (MLGWAS) |
| plotMDT | Plot MDT objects |
| plotMLGWAS | MLGWAS Plots |
| readVcfDir | Reads directory of VCF files |
| selectMDT | Retrieve annotations from MDT objects. |
| summaryMLGWAS | Summary of MLGWAS Performance, Feature Importance and Errors |
| trainClassifier | Train Classifier for MDT |
| trainClassifiers | Calls trainClassifier for different combination of... |
| vcfsToMDT | Convert a list of VCF objects into an MDT object |
