Man pages for USCDTG/tLOH
Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations
| aggregateCHRPlot | Visualization of data output from the tLOHCalc function,... |
| alleleFrequencyPlot | Visualization of data output from the tLOHCalc function |
| documentErrorRegions | Identification of Errors |
| hiddenMarkovAnalysis | Run Multi-Step HMM Analysis on tLOHCalcUpdate output |
| humanGBMsampleAC | Imported dataset of a human glioblastoma spatial... |
| initialStartProbabilities | Imported dataset of sample start probabilities for... |
| marginalLikelihoodM1 | Marginal M1 Calculation |
| marginalLikelihoodM2 | Marginal M2 Calculation |
| marginalM1Calc | Calculate marginal of Model 1 |
| marginalM2CalcBHET | Calculation of marginal M2 het |
| marginalM2CalcBLOH | Marginal M2 Calculation |
| modePeakCalc | Calculation of mode peak |
| prepareHMMdataframes | Prepare dataframes for HMM analysis |
| regionAnalysis | Summary of HMM Regions |
| regionFinalize | Summary of HMM Regions |
| removeOutlierFromCalc | Removes outliers |
| runHMM_1 | Step 1 of HMM process |
| runHMM_2 | Step 2 of HMM process |
| runHMM_3 | Step 3 of HMM process |
| splitByChromosome | Split dataframe into individual chromosome dataframes |
| summarizeRegions1 | Step 1 of region summary |
| summarizeRegions2 | Step 2 of region summary |
| tLOHCalc | Assement of evidence for LOH in clusters from spatial... |
| tLOHCalcUpdate | Assement of evidence for LOH in clusters from spatial... |
| tLOHDataImport | Import VCF for tLOHCalc |
