allele.marq | alleles at markers |
corresp | correspondance |
data.test | data.test |
depart.LD | starting values for the optimization of HAPimLD method |
depart.LDL | starting values for the optimization of HAPimLDL method |
descendant.pere | first and last indexes of each sire progeny |
distance.marqueurs | distance of markers |
distance.test | localisation of test positions |
esp.freq.hap | expectation of extended haplotype frequencies |
freq.all | allelic frequencies |
haldanem1 | recombination rate |
hapim.LD.add | HAPimLD method |
hapim.LDL.add | HAPimLDL method |
HAPim-package | HAPim |
haplomax.add | HaploMax method in unrelated population |
haplomax.HS.add | HaploMax method in half-sib family design |
moyenne.pere | average of performances per sire |
obj.haplomax.add | analysis of variance of the HaploMax method |
obj.haplomax.HS.add | Analysis of variance of the HaploMmax method in half-sib... |
obj.LD.add | log-likelihood value of HAPimLD method under H1 |
obj.LD.add.H0 | log-likelihood value of HAPimLD method under H0 |
obj.LDL.add | log-likelihood value of the HAPimLDL method under H1 |
obj.LDL.add.H0 | log-likelihood value of the HAPimLDL method under H0 |
pi.hap | haplotype frequencies |
pi.hap.NI | haplotype frequencies |
poids.D | poids.D |
proba.DL | conditional probabilities |
proba.DL.diplotype | probabilities due to linkage disequilibrium |
recode.hap | recoding of haplotypes |
retrouve.all | haplotype reconstruction |
structure.hap | Structure |
vrais.LD.add | log likelihood of HAPIimLD method under H1 |
vrais.LDL.add | log likelihood of HAPimLDL method under H1 |
vrais.LDL.add.pere | intra-sire log likelihood of HAPimLDL method under H1. |
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