The genetics Package

8 LDValue- p B is defined as the observed probability of allele ’B’ for marker 2, and- p b = 1 − p B is defined as the observed probability of allele ’b’ for marker 2, and- p AB is defined as the probability of the marker allele pair ’AB’.For genotype data, AB/ab cannot be distinguished from aB/Ab. Consequently, we estimate p ABusing maximum likelihood and use this value in the computations.LD.genotype returns a 5 element list:callDDprimecorrnobschisqp.valuethe matched callLinkage disequilibrium estimateScaled linkage disequilibrium estimateCorrelation coefficientNumber of observationsChi-square statistic for linkage equilibrium (i.e., D=D’=corr=0)Chi-square p-value for marker independenceLD.data.frame returns a list with the same elements, but each element is a matrix where theupper off-diagonal elements contain the estimate for the corresponding pair of markers. The othermatrix elements are NA.Author(s)See AlsoGregory R. Warnes 〈warnes@bst.rochester.edu〉genotype, HWE.testExamplesg1