HapIM


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Documentation for package ‘HAPim’ version 1.3

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HAPim-package HAPim
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 HAPim
hapim.LD.add HAPimLD method
hapim.LDL.add HAPimLDL method
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 family design
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.