Man pages for CostaLab/sigurd
Single cell Genotyping Using RNA Data
| 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 |
| char_to_numeric | char_to_numeric |
| ClonalDefinition | Defining clones. |
| ClonalDiversity | Determining the clonal diversity. |
| combine_NAMES | combine_NAMES |
| CombineSEobjects | CombineSEobjects |
| combine_SparseMatrix | combine_sparseMatrix |
| computeAFMutMatrix | computeAFMutMatrix |
| Enrichment_FisherTest | Enrichment_FisherTest |
| Filtering | Filtering the loaded genotyping data. |
| Filtering_VAF_Threshold | Filtering_VAF_Threshold |
| getAltMatrix | getAltMatrix |
| GetCellInfoPerVariant | We get the variant information per cell. |
| get_consensus | get_consensus |
| getMutMatrix | getMutMatrix |
| getReadMatrix | Get the counts for a specific base over all positions. |
| getRefMatrix | getRefMatrix |
| GetVariantInfo | GetVariantInfo |
| HeatmapVoi | HeatmapVoi |
| LoadingMAEGATK_typewise | LoadingMAEGATK_typewise |
| LoadingMGATK_typewise | LoadingMGATK_typewise |
| LoadingRawMatrix_typewise | LoadingRawMatrix_typewise |
| LoadingVarTrix_typewise | LoadingVarTrix_typewise |
| LoadingVCF_typewise | LoadingVCF_typewise |
| load_object | load_object |
| Merging_SE_list | Merging list of SummarizedExperiment objects. |
| RowWiseSplit | RowWiseSplit |
| save_object | save_object |
| sdiv | Division of sparse matrix. |
| 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 |
