Constructor | Description |
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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)
|
Modifier and Type | Method | Description |
---|---|---|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for the imputer
|
double[][][] |
impute(double[][][] callprobs,
int[][][] readCounts) |
Imputes a genotype table
|
java.util.List<SingleGenotypeProbability> |
impute(double[][][] callprobs,
int[][][] readCounts,
java.util.List<SingleGenotypeProbability> maskedprobs,
java.util.List<SingleGenotypeMasked> list) |
Imputes a list of genotypes.
|
public KnniLDProb(int k, int l, int knownDepth)
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 probabilitypublic KnniLDProb(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic double[][][] impute(double[][][] callprobs, int[][][] readCounts)
Imputer
public java.util.List<SingleGenotypeProbability> impute(double[][][] callprobs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Imputer
impute
in interface Imputer
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