net.maizegenetics.stats.linearmodels

Class ModelEffectUtils

java.lang.Object

net.maizegenetics.stats.linearmodels.ModelEffectUtils

public class ModelEffectUtils
extends Object

Method Summary

Modifier and Type	Method and Description
static <T> int[]	getIntegerLevels(ArrayList<T> originalLevels)
static <T> int[]	getIntegerLevels(ArrayList<T> originalLevels, ArrayList<T> ids)
static int[]	getIntegerLevels(byte[] genotypes, ArrayList<Byte> ids)
static int[]	getIntegerLevels(int[] originalLevels)
static int[]	getIntegerLevels(Object[] originalLevels)
static <T> int[]	getIntegerLevels(T[] originalLevels, ArrayList<T> ids)
static int[]	getIntegerLevelsSortedByGenotype(String[] originalLevels, ArrayList<String> ids)
static double[]	getNumericCodingForAdditiveModel(byte[] marker, byte allele)
static double[]	getNumericCodingForAdditiveModel(Object[] marker, String allele)
static DoubleMatrix	getXtY(ModelEffect X, ModelEffect Y)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getXtY

public static DoubleMatrix getXtY(ModelEffect X,
                                  ModelEffect Y)

getIntegerLevels

public static int[] getIntegerLevels(Object[] originalLevels)

getIntegerLevels

public static <T> int[] getIntegerLevels(T[] originalLevels,
                                         ArrayList<T> ids)

getIntegerLevelsSortedByGenotype

public static int[] getIntegerLevelsSortedByGenotype(String[] originalLevels,
                                                     ArrayList<String> ids)

getIntegerLevels

public static int[] getIntegerLevels(byte[] genotypes,
                                     ArrayList<Byte> ids)

Parameters:

genotypes - a byte array of genotypes

ids - an empty array list that will hold the Bytes corresponding to each level

Returns:

these genotypes translated into factor levels. On return, ids will hold the Byte labels for each level. Levels will be sorted with homozygotes first then heterozygotes.

getIntegerLevels

public static <T> int[] getIntegerLevels(ArrayList<T> originalLevels,
                                         ArrayList<T> ids)

getIntegerLevels

public static <T> int[] getIntegerLevels(ArrayList<T> originalLevels)

getIntegerLevels

public static int[] getIntegerLevels(int[] originalLevels)

getNumericCodingForAdditiveModel

public static double[] getNumericCodingForAdditiveModel(Object[] marker,
                                                        String allele)

getNumericCodingForAdditiveModel

public static double[] getNumericCodingForAdditiveModel(byte[] marker,
                                                        byte allele)

Parameters:

marker - the genotypes for a taxon at all sites as bytes

allele - the allele that should be coded as 1. all others will be 0

Returns:

a vector of values (0,1,2) that encode genotypes equal to the dosage of allele