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

Description Usage Arguments Value Author(s) References See Also

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.

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

DL.chrom2, desc.pere, mean.gene)

`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.

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

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

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.

moyenne.pere, descendant.pere, proba.DL

HAPim documentation built on May 2, 2019, 12:10 p.m.