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.

AuthorS. Dejean, N. Oumouhou, D. Estivals, B. Mangin
Date of publication2012-10-29 08:57:07
MaintainerBrigitte Mangin <brigitte.mangin@toulouse.inra.fr>
LicenseGPL
Version1.3

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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