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C

calculate(byte[][]) - Method in class Correlation.Correlation
Calculates all-against-all LD
calculate(byte[], byte[]) - Method in class Correlation.Correlation
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
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
Constructor
changeData(byte[][]) - Method in class Files.PlinkNumeric
Create a new instance similar to this one but with different genotype data
changeData(byte[][]) - Method in class Files.PlinkPed
Create a new instance similar to this one but with different genotype data
changeData(byte[][], List<String>, List<String>) - Method in class Files.PlinkNumeric
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
Impute missing data
compute(byte[][]) - Method in class Methods.KnniLD
Impute missing data
compute(byte[][]) - Method in class Methods.Mode
Impute missing data
compute(byte[][], double[][]) - Method in class Methods.Knni
Impute missing data
Correlation - package Correlation
Provides classes for calculating LD using different methods.
Correlation - Class in Correlation
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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