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C
- calculate(byte[][]) - Method in class Correlation.Correlation
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Calculates all-against-all LD
- calculate(byte[], byte[]) - Method in class Correlation.Correlation
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Calculates LD between two SNPs
- calculate(byte[], byte[]) - Method in class Correlation.EM
- calculate(byte[], byte[]) - Method in class Correlation.Pearson
- CalculatedSimilar - Class in Similarity
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Calculates the most similar sites to a site when needed (with a cache of the last site calculated)
- CalculatedSimilar(Correlation, byte[][], int) - Constructor for class Similarity.CalculatedSimilar
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Constructor
- changeData(byte[][]) - Method in class Files.PlinkNumeric
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Create a new instance similar to this one but with different genotype data
- changeData(byte[][]) - Method in class Files.PlinkPed
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Create a new instance similar to this one but with different genotype data
- changeData(byte[][], List<String>, List<String>) - Method in class Files.PlinkNumeric
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Creates a new PlinkNumeric instance with the same meta information as this instance but different data
- changeFormat(FormatDefinition, Position, String[]) - Method in class Files.VCFData.Data
- CHARACTER - Files.VCFData.DataType
- clone() - Method in class Files.VCF
- clone() - Method in class Files.VCFData.Data
- clone() - Method in class Files.VCFData.Meta
- clone() - Method in class Files.VCFData.Position
- compare(Integer, Integer) - Method in class Utils.SortByIndexDouble
- compareTo(SampleSnp) - Method in class Mask.SampleSnp
- compute(byte[][]) - Method in class Methods.Knni
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Impute missing data
- compute(byte[][]) - Method in class Methods.KnniLD
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Impute missing data
- compute(byte[][]) - Method in class Methods.Mode
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Impute missing data
- compute(byte[][], double[][]) - Method in class Methods.Knni
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Impute missing data
- Correlation - package Correlation
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Provides classes for calculating LD using different methods.
- Correlation - Class in Correlation
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Abstract class for calculating LD.
- count() - Method in class Files.VCFData.Data
- countIf(FormatDefinition, String) - Method in class Files.VCFData.Data
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