Man pages for smgogarten/SeqVarTools
Tools for variant data
| alleleFrequency | Allele frequency |
| allele-methods | Extract allele information from a GDS object |
| alternateAlleleDetection | alternateAlleleDetection |
| applyMethod | Apply method to GDS object |
| chromWithPAR | Identify pseudoautosomal region |
| countSingletons | Count singletons |
| duplicateDiscordance | Duplicate discordance |
| getGenotype | Get genotype data |
| getVariableLengthData | Get variable-length data |
| heterozygosity | Heterozygosity and Homozygosity |
| hwe | Exact test for Hardy-Weinberg equilibrium |
| imputedDosage | Get imputed dosage |
| inbreedCoeff | Inbreeding coefficient |
| isSNV | Flag single nucleotide variants |
| isVariant | Locate variant samples across sites |
| Iterator-class | Iterators |
| meanBySample | Mean value by sample |
| mendelErr | Mendelian errors |
| missingGenotypeRate | Missing genotype rate |
| pca | Principal Component Analysis |
| pedigree | Pedigree for example data |
| refFrac | Reference allele fraction |
| regression | Linear or logistic regression |
| SeqVarData-class | SeqVarData |
| SeqVarTools-package | Tools for Variant Analysis |
| setVariantID | Change the variant ID of a GDS file |
| titv | Transition/Transversion Ratio |
| variantInfo | Variant info |
