Function reference • sigurd

All functions

AllelFrequencyFoldChange(): AllelFrequencyFoldChange

AmpliconSupplementing(): Supplementing scRNAseq values with Amplicon values

CalculateAlleleFrequency(): Calculating the Minor Allele Frequency.

CalculateAltReads(): CalculateAltReads

CalculateConsensus(): CalculateConsensus

CalculateCorrelationPValue(): Correlating the SNVs

CalculateCoverage(): CalculateCoverage

CalculateFisherTestPValue(): CalculateFisherTestPValue

CalculateForwardReads(): CalculateForwardReads

CalculateQuality(): CalculateQuality

CalculateRefReads(): CalculateRefReads

CalculateReverseReads(): CalculateReverseReads

CalculateStrandCorrelation(): CalculateStrandCorrelation

CallSupport(): CallSupport

ClonalDefinition(): Defining clones.

ClonalDefinition_Singular(): Defining a single clone using multiple variants.

ClonalDiversity(): Determining the clonal diversity.

CombineSEobjects(): CombineSEobjects

Enrichment_FisherTest(): Enrichment_FisherTest

Filtering(): Filtering the loaded genotyping data.

Filtering_VAF_Threshold(): Filtering_VAF_Threshold

GetCellInfoPerVariant(): We get the variant information per cell.

GetVariantInfo(): GetVariantInfo

HeatmapVoi(): HeatmapVoi

LoadingMAEGATK_typewise(): LoadingMAEGATK_typewise

LoadingMGATK_typewise(): LoadingMGATK_typewise

LoadingRawMatrix_typewise(): LoadingRawMatrix_typewise

LoadingVCF_typewise(): LoadingVCF_typewise

LoadingVarTrix_typewise(): LoadingVarTrix_typewise

Merging_SE_list(): Merging list of SummarizedExperiment objects.

RowWiseSplit(): RowWiseSplit

SeparatingMatrixToList(): SeparatingMatrixToList

SetVariantInfo(): SetVariantInfo

UMIQC(): UMIQC

UMI_seq(): UMI_seq

VariantBurden(): VariantBurden

VariantCloneSizeThresholding(): VariantCloneSizeThresholding

VariantCorrelationHeatmap(): VariantCorrelationHeatmap

VariantFisherTestHeatmap(): VariantFisherTestHeatmap

VariantQuantileThresholding_Combined(): VariantQuantileThresholding_Combined

VariantSelection_Group(): VariantSelection_Group

VariantSelection_Quantile(): VariantSelection_Quantile

VariantSelection_TopCells(): VariantSelection_TopCells

VariantSelection_VMR(): VariantSelection_VMR

VariantSelection_VMR_Group(): VariantSelection_VMR_Group

VariantWiseCorrelation(): VariantWiseCorrelation

VariantWiseFisherTest(): VariantWiseFisherTest

char_to_numeric(): char_to_numeric

combine_NAMES(): combine_NAMES

combine_SparseMatrix(): combine_sparseMatrix

computeAFMutMatrix(): computeAFMutMatrix

getAltMatrix(): getAltMatrix

getMutMatrix(): getMutMatrix

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

sdiv(): Division of sparse matrix.