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.

Install the latest version of this package by entering the following in R:
install.packages("HAPim")
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

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.

Functions

allele.marq Man page
corresp Man page
data.test Man page
depart.LD Man page
depart.LDL Man page
descendant.pere Man page
distance.marqueurs Man page
distance.test Man page
esp.freq.hap Man page
freq.all Man page
haldanem1 Man page
HAPim Man page
hapim.LD.add Man page
hapim.LDL.add Man page
HAPim-package Man page
haplomax.add Man page
haplomax.HS.add Man page
moyenne.pere Man page
obj.haplomax.add Man page
obj.haplomax.HS.add Man page
obj.LD.add Man page
obj.LD.add.H0 Man page
obj.LDL.add Man page
obj.LDL.add.H0 Man page
pi.hap Man page
pi.hap.NI Man page
poids.D Man page
proba.DL Man page
proba.DL.diplotype Man page
recode.hap Man page
retrouve.all Man page
structure.hap Man page
vrais.LD.add Man page
vrais.LDL.add Man page
vrais.LDL.add.pere Man page

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

Please suggest features or report bugs with the GitHub issue tracker.

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