# Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

## Documentation for package ‘tLOH’ version 1.14.0

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

## Help Pages

aggregateCHRPlot | Visualization of data output from the tLOHCalc function, aggregated per chromosome
alleleFrequencyPlot | Visualization of data output from the tLOHCalc function
cols | Removes outliers
dataframe | Removes outliers
documentErrorRegions | Identification of Errors
hiddenMarkovAnalysis | Run Multi-Step HMM Analysis on tLOHCalcUpdate output
humanGBMsampleAC | Imported dataset of a human glioblastoma spatial transcriptomics sample processed with tLOHImportData.
initialStartProbabilities | Imported dataset of sample start probabilities for hiddenMarkovAnalysis
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
newValue | Removes outliers
prepareHMMdataframes | Prepare dataframes for HMM analysis
regionAnalysis | Summary of HMM Regions
regionFinalize | Summary of HMM Regions
removeOutlierFromCalc | Removes outliers
rows | 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 transcriptomics data
tLOHCalcUpdate | Assement of evidence for LOH in clusters from spatial transcriptomics allele count data
tLOHDataImport | Import VCF for tLOHCalc