Package Imputers
Class KnniLDProb
- java.lang.Object
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- Imputers.KnniLDProb
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Constructor Summary
Constructors Constructor Description KnniLDProb(int k, int l, int knownDepth)
Creates an object to perform LD-kNNi with given values of k and l.KnniLDProb(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for the imputerdouble[][][]
impute(double[][][] callprobs, int[][][] readCounts)
Imputes a genotype tablejava.util.List<SingleGenotypeProbability>
impute(double[][][] callprobs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Imputes a list of genotypes.
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Constructor Detail
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KnniLDProb
public KnniLDProb(int k, int l, int knownDepth)
Creates an object to perform LD-kNNi with given values of k and l.- Parameters:
k
- The value of k to be usedl
- The value of l to be usedknownDepth
- At depths at or above this no imputation is done and the imputed probability is the same as the called probability
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KnniLDProb
public KnniLDProb(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)- Parameters:
params
- The config
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Method Detail
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impute
public double[][][] impute(double[][][] callprobs, int[][][] readCounts)
Description copied from interface:Imputer
Imputes a genotype table
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impute
public java.util.List<SingleGenotypeProbability> impute(double[][][] callprobs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Description copied from interface:Imputer
Imputes a list of genotypes. Used to calculate accuracy. Need both unmasked probs (probs) and masked probs (maskedprobs) so that the calculation for each genotype is independent (i.e. using the full reads for the other masked genotypes if they're used in the imputation calculation).- Specified by:
impute
in interfaceImputer
- Parameters:
callprobs
- Genotype probabilities (from a caller)readCounts
- Read counts for each genotypemaskedprobs
- Genotype probabilities (from a caller) using masked readslist
- List of genotypes to impute- Returns:
- List of imputed genotype probabilities
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