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

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Documentation for package ‘tLOH’ version 1.17.0

• 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