vrais.LDL.add: log likelihood of HAPimLDL method under H1

Description Usage Arguments Value Author(s) References See Also

Description

The function calculates the value of 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

1
2
3
4
vrais.LDL.add(moyenne.pere, alpha.Q, s, CD, perf, PLA, DL.m, 
DL.chrom1, 

DL.chrom2, desc.pere, 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 (number of individuals) which contains transmission probabilities at a single test position.

DL.m

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

DL.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.

DL.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.

desc.pere

results provided by descendant.pere() function, numeric matrix (number of sires x 2) which gives for each sire, the first and last indexes of its progeny.

mean.gene

parameter of the performance mean.

Value

The returned value is the value of 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, descendant.pere, proba.DL


HAPim documentation built on May 30, 2017, 3:13 a.m.

Search within the HAPim package
Search all R packages, documentation and source code