Tools for variant data


[Up] [Top]

Documentation for package ‘SeqVarTools’ version 1.12.0

Help Pages

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