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

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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.

Author(s)

S. Dejean, N. Oumouhou, D. Estivals, B. Mangin

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

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