SeqVarTools-package | Tools for Variant Analysis |
allele-methods | Extract allele information from a GDS object |
alleleCount | Allele frequency |
alleleCount-method | Allele frequency |
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 |
chromWithPAR | Identify pseudoautosomal region |
chromWithPAR-method | Identify pseudoautosomal region |
countSingletons | Count singletons |
countSingletons-method | Count singletons |
currentRanges | Iterators |
currentRanges-method | Iterators |
currentVariants | Iterators |
currentVariants-method | Iterators |
duplicateDiscordance | Duplicate discordance |
duplicateDiscordance-method | Duplicate discordance |
expandedAltDosage | Get genotype data |
expandedAltDosage-method | Get genotype data |
expandedVariantIndex | Variant info |
expandedVariantIndex-method | Variant info |
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 |
imputedDosage | Get imputed dosage |
imputedDosage-method | Get imputed dosage |
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 |
iterateFilter | Iterators |
iterateFilter-method | Iterators |
lastFilter | Iterators |
lastFilter-method | Iterators |
lastFilter<- | Iterators |
lastFilter<--method | Iterators |
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 |
resetIterator | Iterators |
resetIterator-method | Iterators |
sampleData | SeqVarData |
sampleData-method | SeqVarData |
sampleData<- | SeqVarData |
sampleData<--method | SeqVarData |
SeqVarBlockIterator | Iterators |
SeqVarBlockIterator-class | Iterators |
SeqVarData | SeqVarData |
SeqVarData-class | SeqVarData |
SeqVarIterator | Iterators |
SeqVarIterator-class | Iterators |
SeqVarListIterator | Iterators |
SeqVarListIterator-class | Iterators |
SeqVarRangeIterator | Iterators |
SeqVarRangeIterator-class | Iterators |
SeqVarTools | Tools for Variant Analysis |
SeqVarWindowIterator | Iterators |
SeqVarWindowIterator-class | Iterators |
setVariantID | Change the variant ID of a GDS file |
show-method | Iterators |
show-method | SeqVarData |
titv | Transition/Transversion Ratio |
titv-method | Transition/Transversion Ratio |
validateSex | SeqVarData |
validateSex-method | SeqVarData |
variantBlock | Iterators |
variantBlock-method | Iterators |
variantData | SeqVarData |
variantData-method | SeqVarData |
variantData<- | SeqVarData |
variantData<--method | SeqVarData |
variantFilter | Iterators |
variantFilter-method | Iterators |
variantInfo | Variant info |
variantInfo-method | Variant info |
variantRanges | Iterators |
variantRanges-method | Iterators |