alun.genio
Interface BasicGeneticData

All Superinterfaces:

ParameterData, PedigreeData

All Known Subinterfaces:

GeneticDataSource

All Known Implementing Classes:

LinkageInterface

public interface BasicGeneticData
extends ParameterData, PedigreeData

Method Summary

java.lang.String	id(int i) Returns the string representing the ith individual in the pedigree data.
double[][]	penetrance(int i, int j) Returns the penetrance function for the ith person in the list at the jth genetic locus.

Methods inherited from interface alun.genio.ParameterData

alleleFreqs, getFemaleRecomFrac, getMaleRecomFrac, nAlleles, nLoci

Methods inherited from interface alun.genio.PedigreeData

kids, ma, nIndividuals, nuclearFamilies, pa

Method Detail

id

java.lang.String id(int i)

Returns the string representing the ith individual in the pedigree data.

penetrance

double[][] penetrance(int i,
                      int j)

Returns the penetrance function for the ith person in the list at the jth genetic locus. This is a matrix of dimension nAlleles(j) x nAlleles(j) where the entry at row a, column b is the probability of the individual's observed phenotype given that they have allele number a on the paternal chromosome and allele number b on the maternal chromosome. Again, phenotype is used in a very general way so this function is also used to express genotypic information. If an individual i is observed with genotype (x,y) at locus j then penetrance(i,j)[x,y] = penetrance(i,j)[y,x] = 1 with zeros elsewhere. If the locus is not perfectly co-dominant, or there is error in the observation, this should be expressed appropriately in this matrix. If no information is present for the ith individual at the jth locus this method can return null.