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| SeqVarTools-package | Tools for Variant Analysis |
| allele-methods | Extract allele information from a GDS object |
| alleleDosage | Get genotype data |
| alleleDosage-method | Get genotype data |
| alleleFrequency | Allele frequency |
| alleleFrequency-method | Allele frequency |
| altChar | Extract allele information from a GDS object |
| altChar-method | Extract allele information from a GDS object |
| altDosage | Get genotype data |
| altDosage-method | Get genotype data |
| alternateAlleleDetection | alternateAlleleDetection |
| alternateAlleleDetection-method | alternateAlleleDetection |
| applyMethod | Apply method to GDS object |
| applyMethod-method | Apply method to GDS object |
| countSingletons | Count singletons |
| countSingletons-method | Count singletons |
| duplicateDiscordance | Duplicate discordance |
| duplicateDiscordance-method | Duplicate discordance |
| getGenotype | Get genotype data |
| getGenotype-method | Get genotype data |
| getGenotypeAlleles | Get genotype data |
| getGenotypeAlleles-method | Get genotype data |
| getVariableLengthData | Get variable-length data |
| getVariableLengthData-method | Get variable-length data |
| granges | SeqVarData |
| granges-method | SeqVarData |
| heterozygosity | Heterozygosity and Homozygosity |
| heterozygosity-method | Heterozygosity and Homozygosity |
| hethom | Heterozygosity and Homozygosity |
| hethom-method | Heterozygosity and Homozygosity |
| homozygosity | Heterozygosity and Homozygosity |
| homozygosity-method | Heterozygosity and Homozygosity |
| hwe | Exact test for Hardy-Weinberg equilibrium |
| hwe-method | Exact test for Hardy-Weinberg equilibrium |
| inbreedCoeff | Inbreeding coefficient |
| inbreedCoeff-method | Inbreeding coefficient |
| isSNV | Flag single nucleotide variants |
| isSNV-method | Flag single nucleotide variants |
| isVariant | Locate variant samples across sites |
| isVariant-method | Locate variant samples across sites |
| meanBySample | Mean value by sample |
| meanBySample-method | Mean value by sample |
| mendelErr | Mendelian errors |
| mendelErr-method | Mendelian errors |
| missingGenotypeRate | Missing genotype rate |
| missingGenotypeRate-method | Missing genotype rate |
| nAlleles | Extract allele information from a GDS object |
| nAlleles-method | Extract allele information from a GDS object |
| pca | Principal Component Analysis |
| pca-method | Principal Component Analysis |
| pedigree | Pedigree for example data |
| refChar | Extract allele information from a GDS object |
| refChar-method | Extract allele information from a GDS object |
| refDosage | Get genotype data |
| refDosage-method | Get genotype data |
| refFrac | Reference allele fraction |
| refFrac-method | Reference allele fraction |
| refFracOverHets | Reference allele fraction |
| refFracOverHets-method | Reference allele fraction |
| refFracPlot | Reference allele fraction |
| refFracPlot-method | Reference allele fraction |
| regression | Linear or logistic regression |
| regression-method | Linear or logistic regression |
| sampleData | SeqVarData |
| sampleData-method | SeqVarData |
| sampleData<- | SeqVarData |
| sampleData<--method | SeqVarData |
| SeqVarData | SeqVarData |
| SeqVarData-class | SeqVarData |
| SeqVarTools | Tools for Variant Analysis |
| setVariantID | Change the variant ID of a GDS file |
| titv | Transition/Transversion Ratio |
| titv-method | Transition/Transversion Ratio |
| variantData | SeqVarData |
| variantData-method | SeqVarData |
| variantData<- | SeqVarData |
| variantData<--method | SeqVarData |