HAPim (version 1.3)

vrais.LDL.add.pere: intra-sire log likelihood of HAPimLDL method under H1.

Description

The function calculates the value of intra-sire log likelihood of HAPimLDL method under alternative hypothesis H1. It can be viewed as an internal function. The user does not have to call it by himself.

Usage

vrais.LDL.add.pere(moyenne.pere, alpha.Q, s, CD, perf, PLA, LD.m, LD.chrom1,
LD.chrom2, mean.gene)

Arguments

moyenne.pere

results provided by moyenne.pere() function, mean of half-sib family performances.

alpha.Q

parameter of QTL effect.

s

parameter of the error variance.

CD

numeric vector of length=number of individuals which contains the CD of individuals. var(perf$_i$)=s/CD$^2_i$

perf

numeric vector of length=number of individuals which contains the performances of individuals.

PLA

numeric vector of length=number of individuals which contains transmission probabilities at a single test position

LD.m

results provided by proba.DL() function, numeric vector of length=number of individuals which contains probabilities due to linkage disequilibrium on dam.

LD.chrom1

results provided by proba.DL() function, numeric vector of length=number of individuals which contains probabilities due to linkage disequilibrium on the first chromosome of sire.

LD.chrom2

results provided by proba.DL() function, numeric vector of length=number of individuals which contains probabilities due to linkage disequilibrium on the second chromosome of sire.

mean.gene

parameter of performance mean.

Value

The returned value is the value of intra-sire log likelihood of HAPimLDL method under alternative hypothesis H1.

References

publication to be submitted: C. Cierco-Ayrolles, S. Dejean, A. Legarra, H. Gilbert, T. Druet, F. Ytournel, D. Estivals, N. Oumouhou and B. Mangin. Combining linkage analysis and linkage disequilibrium for QTL fine mapping in animal pedigrees.

See Also

moyenne.pere, proba.DL