Interface | Description |
---|---|
AlleleProbs |
Interface
AlleleProbs represents per-haplotype allele
probabilities for a list of samples. |
GeneticMap |
Interface
GeneticMap represents a genetic map for one or more
chromosomes. |
GenotypeValues |
Interface
GenotypeValues represents a value for each
possible genotype for each sample at each marker. |
HapAlleleProbs |
Interface
HapAlleleProbs stores allele probabilities for
a haplotype. |
Class | Description |
---|---|
BasicAlleleProbs |
Class
BasicAlleleProbs stores per-haplotype allele probabilities
for a list of samples. |
BasicGenotypeValues |
Class
BasicGenotypeValues stores values for each possible
genotype for each sample at each marker. |
ConstrainedAlleleProbs |
Class
ConstrainedAlleleProbs is a wrapper for an
AlleleProbs instance that changes the wrapped haplotype allele
probabilities for a subset of markers. |
CurrentData |
Class
CurrentData represents input data for the current marker
window. |
HapPairSampler |
Class
HapPairSampler samples haplotype pairs and
estimates posterior genotype probabilities. |
LiAndStephensHapSampler |
Class
LiAndStephensHapSampler estimates posterior allele probabilities. |
LowMemHapAlleleProbs |
Class
LowMemHapAlleleProbs stores allele probabilities for
a haplotype. |
Main |
Class
Main is the entry class for the Beagle program. |
MainHelper |
Class
MainHelper is an auxiliary class with methods called by
the main.Main class. |
NuclearFamilies |
Class
NuclearFamilies stores parent-offspring relationships
in a list of samples. |
Par |
Class
Parameters represents the parameters for a Beagle analysis. |
PlinkGeneticMap |
Class
PlinkGeneticMap represents a genetic map derived
from a PLINK map file with map positions in cM units for one or more
chromosomes. |
PositionMap |
Class
PositionMap represents a genetic map obtained by
multiplying chromosome position by a scale factor. |
RecombHapPairSampler |
Class
RecombHapPairSamples samples haplotype pairs and
estimates posterior genotype probabilities using a haplotype frequency
model that permits transitions between any two states at adjacent markers. |
RevGenotypeValues |
Class
RevGenotypeValues is a wrapper for a GenotypeValues
instance. |
RunStats |
Class
RunStats contains methods for storing and printing
statistics describing a Beagle analysis. |
SampleGenotypeValues |
Class
SampleGenotypeValues stores a value for each possible
genotype at each marker for one sample. |
SampleHapPairAlleleProbs |
Class
SampleHapPairAlleleProbs is a wrapper for a
SampleHapPairs instance. |
WindowWriter |
Class
WindowWriter writes VCF and IBD output data. |