Function reference
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AmpliconSupplementing()
- Supplementing scRNAseq values with Amplicon values
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CalculateAlleleFrequency()
- Calculating the Minor Allele Frequency.
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CalculateAltReads()
- CalculateAltReads
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CalculateConsensus()
- CalculateConsensus
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CalculateCorrelationPValue()
- Correlating the SNVs
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CalculateCoverage()
- CalculateCoverage
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CalculateFisherTestPValue()
- CalculateFisherTestPValue
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CalculateQuality()
- CalculateQuality
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CalculateStrandCorrelation()
- CalculateStrandCorrelation
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ClonalDefinition()
- Defining clones.
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ClonalDiversity()
- Determining the clonal diversity.
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CombineSEobjects()
- CombineSEobjects
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Enrichment_FisherTest()
- Enrichment_FisherTest
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Filtering()
- Filtering the loaded genotyping data.
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GetCellInfoPerVariant()
- We get the variant information per cell.
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GetVariantInfo()
- GetVariantInfo
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HeatmapVoi()
- HeatmapVoi
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LoadingMAEGATK_typewise()
- LoadingMAEGATK_typewise
-
LoadingVCF_typewise()
- LoadingVCF_typewise
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LoadingVarTrix_typewise()
- LoadingVarTrix_typewise
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Merging_SE_list()
- Merging list of SummarizedExperiment objects.
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RowWiseSplit()
- RowWiseSplit
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SeparatingMatrixToList()
- SeparatingMatrixToList
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SetVariantInfo()
- SetVariantInfo
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UMIQC()
- UMIQC
-
UMI_seq()
- UMI_seq
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VariantBurden()
- VariantBurden
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VariantCloneSizeThresholding()
- VariantCloneSizeThresholding
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VariantCorrelationHeatmap()
- VariantCorrelationHeatmap
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VariantFisherTestHeatmap()
- VariantFisherTestHeatmap
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VariantQuantileThresholding()
- VariantQuantileThresholding
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VariantWiseCorrelation()
- VariantWiseCorrelation
-
VariantWiseFisherTest()
- VariantWiseFisherTest
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char_to_numeric()
- char_to_numeric
-
combine_NAMES()
- combine_NAMES
-
combine_SparseMatrix()
- combine_sparseMatrix
-
computeAFMutMatrix()
- computeAFMutMatrix
-
getAltMatrix()
- getAltMatrix
-
getMutMatrix()
- getMutMatrix
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getReadMatrix()
- Get the counts for a specific base over all positions.
-
getRefMatrix()
- getRefMatrix
-
get_consensus()
- get_consensus
-
load_object()
- load_object
-
save_object()
- save_object
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sdiv()
- Division of sparse matrix.