HAPim: HapIM

The package provides a set of functions whose aim is to propose 4 methods of QTL detection. HAPimLD is an interval-mapping method designed for unrelated individuals with no family information that makes use of linkage disequilibrium. HAPimLDL is an interval-mapping method for design of half-sib families. It combines linkage analysis and linkage disequilibrium. HaploMax is based on an analysis of variance with a dose haplotype effect. HaploMaxHS is based on an analysis of variance with a sire effect and a dose haplotype effect in half-sib family design. Fundings for the package development were provided to the LDLmapQTL project by the ANR GENANIMAL program and APIS-GENE.

Author
S. Dejean, N. Oumouhou, D. Estivals, B. Mangin
Date of publication
2012-10-29 08:57:07
Maintainer
Brigitte Mangin <brigitte.mangin@toulouse.inra.fr>
License
GPL
Version
1.3

View on CRAN

Man pages

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.

Files in this package

HAPim
HAPim/data
HAPim/data/data.test.rda
HAPim/NAMESPACE
HAPim/man
HAPim/man/haldanem1.Rd
HAPim/man/obj.haplomax.HS.add.Rd
HAPim/man/proba.DL.diplotype.Rd
HAPim/man/retrouve.all.Rd
HAPim/man/proba.DL.Rd
HAPim/man/corresp.Rd
HAPim/man/data.test.Rd
HAPim/man/vrais.LDL.add.Rd
HAPim/man/haplomax.HS.add.Rd
HAPim/man/obj.haplomax.add.Rd
HAPim/man/distance.test.Rd
HAPim/man/pi.hap.Rd
HAPim/man/pi.hap.NI.Rd
HAPim/man/structure.hap.Rd
HAPim/man/depart.LD.Rd
HAPim/man/descendant.pere.Rd
HAPim/man/distance.marqueurs.Rd
HAPim/man/HAPim-package.Rd
HAPim/man/obj.LD.add.H0.Rd
HAPim/man/obj.LDL.add.H0.Rd
HAPim/man/vrais.LD.add.Rd
HAPim/man/allele.marq.Rd
HAPim/man/poids.D.Rd
HAPim/man/obj.LD.add.Rd
HAPim/man/esp.freq.hap.Rd
HAPim/man/moyenne.pere.Rd
HAPim/man/recode.hap.Rd
HAPim/man/vrais.LDL.add.pere.Rd
HAPim/man/depart.LDL.Rd
HAPim/man/hapim.LDL.add.Rd
HAPim/man/freq.all.Rd
HAPim/man/haplomax.add.Rd
HAPim/man/hapim.LD.add.Rd
HAPim/man/obj.LDL.add.Rd
HAPim/DESCRIPTION
HAPim/MD5
HAPim/R
HAPim/R/proba.DL.diplotype.R
HAPim/R/proba.DL.R
HAPim/R/depart.LD.R
HAPim/R/obj.haplomax.HS.add.R
HAPim/R/obj.LDL.add.H0.R
HAPim/R/structure.hap.R
HAPim/R/obj.haplomax.add.R
HAPim/R/vrais.LD.add.R
HAPim/R/obj.LDL.add.R
HAPim/R/vrais.LDL.add.pere.R
HAPim/R/esp.freq.hap.R
HAPim/R/distance.test.R
HAPim/R/haldanem1.R
HAPim/R/freq.all.R
HAPim/R/poids.D.R
HAPim/R/obj.LD.add.H0.R
HAPim/R/vrais.LDL.add.R
HAPim/R/distance.marqueurs.R
HAPim/R/pi.hap.R
HAPim/R/hapim.LD.add.R
HAPim/R/depart.LDL.R
HAPim/R/haplomax.HS.add.R
HAPim/R/haplomax.add.R
HAPim/R/corresp.R
HAPim/R/moyenne.pere.R
HAPim/R/pi.hap.NI.R
HAPim/R/hapim.LDL.add.R
HAPim/R/allele.marq.R
HAPim/R/recode.hap.R
HAPim/R/descendant.pere.R
HAPim/R/obj.LD.add.R
HAPim/R/retrouve.all.R