SeqVarTools-package | Tools for Variant Analysis |
allele-methods | Extract allele information from a GDS object |
alleleFrequency | Allele frequency |
alleleFrequency-method | Allele frequency |
altChar | Extract allele information from a GDS object |
altChar-method | Extract allele information from a GDS object |
applyMethod | Apply method to GDS object |
applyMethod-method | Apply method to GDS object |
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 |
heterozygosity | Heterozygosity and Homozygosity |
heterozygosity-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 |
SeqVarTools | Tools for Variant Analysis |
setVariantID | Change the variant ID of a GDS file |
titv | Transition/Transversion Ratio |
titv-method | Transition/Transversion Ratio |