API for lawremi/VariantTools
Tools for Exploratory Analysis of Variant Calls
| Global functions | |
|---|---|
| %variant_in% | Man page |
| %variant_in%,GenomicRanges,GenomicRanges-method | Man page |
| .codon2trans | Source code |
| .getConcordantCliques | Source code |
| .test | Source code |
| .valid_TallyVariantsParam | Source code |
| AverageNeighborCountFilter | Source code |
| BinomialLRFilter | Source code |
| CallGenotypesParam | Man page Source code |
| CallableInOtherFilter | Source code |
| DepthFETFilter | Man page Source code |
| DistanceToNearestFilter | Source code |
| GenotypeRunVRanges | Source code |
| IndelsNotSupportedFilter | Source code |
| InternalReadPosBinFilter | Source code |
| LowerFrequencyInOtherFilter | Source code |
| MaskFilter | Source code |
| MaxControlFreqFilter | Man page Source code |
| MedianDistFromNearestEndFilter | Source code |
| MinAltDepthFilter | Source code |
| MinTotalDepthFilter | Man page Source code |
| NeighborCountFilter | Source code |
| NonNRefFilter | Source code |
| NonRefFilter | Source code |
| ReadPosCountFilter | Source code |
| ReadPositionTTestFilter | Source code |
| SampleSpecificVariantFilters | Man page Source code |
| SetdiffPositionsFilter | Source code |
| SetdiffVariantsFilter | Man page Source code |
| SingleVariantFilter | Source code |
| StrandFETFilter | Source code |
| TallyVariantsParam | Man page Source code |
| VariantCallingFilters | Man page Source code |
| VariantConcordanceFilters | Source code |
| VariantPostFilters | Man page Source code |
| VariantQAFilters | Man page Source code |
| VariantSanityFilters | Source code |
| VariantTallyParam | Man page |
| addGenotypeRuns | Source code |
| annotateWithControlDepth | Man page Source code |
| calculateConcordanceMatrix | Man page Source code |
| calculatePowerInOther | Source code |
| calculateVariantConcordance | Man page Source code |
| callGenotypes | Man page |
| callGenotypes,TabixFile-method | Man page |
| callGenotypes,VRanges-method | Man page |
| callGenotypesOneRegion | Source code |
| callSampleSpecificVariants | Man page |
| callSampleSpecificVariants,BamFile,BamFile-method | Man page |
| callSampleSpecificVariants,GenomicRanges,GenomicRanges-method | Man page |
| callSampleSpecificVariants,VRanges,VRanges-method | Man page |
| callSampleSpecificVariants,character,character-method | Man page |
| callVariantConcordance | Man page Source code |
| callVariants | Man page |
| callVariants,BamFile-method | Man page |
| callVariants,GenomicRanges-method | Man page |
| callVariants,VRanges-method | Man page |
| callVariants,character-method | Man page |
| callWildtype | Man page Source code |
| caseControlFET | Source code |
| chunkRange | Source code |
| compute_GL | Source code |
| compute_GQ | Source code |
| compute_GT | Source code |
| coverage_H1993 | Man page |
| coverage_H2073 | Man page |
| defaultBPPARAM | Source code |
| extractCoverageForPositions | Man page Source code |
| file_ext_sans_gz | Source code |
| findAverageNeighborCount | Source code |
| fisher_p | Source code |
| fisher_p_vectorized | Source code |
| flankingCycleBreaks | Source code |
| genome_p53 | Man page |
| installed | Source code |
| loadAndComputeGenotypesForRegion | Source code |
| loadVariants | Source code |
| lrtFreqCutoff | Source code |
| matchVariants | Man page Source code |
| mergeVariantInfo | Source code |
| minCallableCoverage | Man page Source code |
| p53 | Man page |
| phred | Source code |
| pileupGRanges | Source code |
| pileupGRangesOverGenome | Source code |
| pileupVariants | Man page Source code |
| postFilterVariants | Man page Source code |
| qaVariants | Man page Source code |
| rawTotalDepth | Source code |
| sanitizeVariants | Source code |
| t.test_welch | Source code |
| tallies_H1993 | Man page |
| tallies_H2073 | Man page |
| tallyVariants | Man page |
| tallyVariants,BamFile-method | Man page |
| tallyVariants,BamFileList-method | Man page |
| tallyVariants,character-method | Man page |
| trans2genome | Source code |
| twoWayTabulate | Source code |
| variantGR2Vcf | Man page Source code |
| variantKeys | Source code |
| variant_intersect | Source code |
| variant_setdiff | Source code |
