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


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Documentation for package ‘tLOH’ version 1.6.0

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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