HAPim (version 1.3)

hapim.LD.add: HAPimLD method

Description

HAPimLD is a method of QTL(Quantitative Trait Loci) detection developed by Boitard et al. (2006). It is an interval-mapping method designed for unrelated individuals with no family information. It is based on a maximum-likelihood calculation and makes use of linkage disequilibrium through a Wright-Fisher modelisation of the population evolution.

Usage

hapim.LD.add(hap.trans.pere, hap.trans.mere, perf, CD, map, position, 
temps.depart, perfectLD, marq.hap.left)

Arguments

hap.trans.pere

character matrix (number of individuals x number of markers) which provides, for each individual, the haplotype transmitted by its father.

hap.trans.mere

character matrix (number of individuals x number of markers) which provides, for each individual, the haplotype transmitted by its mother.

perf

numeric vector of length=number of individuals which contains the performances of individuals.

CD

numeric vector of length=number of individuals which contains the CD of individuals. var(perf$_i$)=error variance/CD$^2_i$

map

numeric vector of length=(number of markers-1) which contains the distance in Morgan between two consecutive markers on the chromosome.

position

numeric vector which contains the distance in Morgan of test positions from the beginning of the chromosome (first marker).

temps.depart

numeric value which provides a start value for the evolution time of the population.

perfectLD

need to be equal to TRUE: linkage disequilibrium is complete between mutated haplotype and Q allele at time 0.

marq.hap.left

(number of markers of the mutated haplotype)/2.

Value

The returned value is a data frame which contains 8 columns:-Test positions-Value of Likelihood Ratio Test (LRT)-Mutated (i.e. associated to Q allele) haplotype-Estimate of the error variance-Estimate of the Q allele effect-Estimate of the time of population evolution-Estimate of the Q allele frequency at time t=0-Estimate of the performance mean

Details

Individual information have to be ranged in the same order in hap.trans.mere, hap.trans.pere, perf, CD.

All distances are assumed to be Haldame's distance in Morgan.

References

Boitard et al. Linkage disequilibrium interval mapping of quantitative trait loci. BMC Genomics (2006) 7:54.

publication to be submitted: C. Cierco-Ayrolles, S. Dejean, A. Legarra, H. Gilbert, T. Druet, F. Ytournel, D. Estivals, N. Oumouhou and B. Mangin. Combining linkage analysis and linkage disequilibrium for QTL fine mapping in animal pedigrees.

Examples

data(data.test)
map=data.test[[1]]
hap.trans.mere=data.test[[2]]
hap.trans.pere=data.test[[3]]
perf=data.test[[6]]
CD=data.test[[7]]


# In this example,marker positions are: 0, 0.010, 0.020, 0.030, 0.040, 0.050, 0.060, 
# 0.070, 0.080, 0.090. 
# We want to test the presence/absence of a QTL between 2 consecutive markers, so

position=c(0.005,0.015,0.025,0.035,0.045,0.055,0.065,0.075,0.085)

# we use a 2 markers-associated haplotype.
marq.hap.left=1

# We assume an evolution of 50 generations.
temps.depart=50
perfectLD=TRUE


hapim.LD.add=hapim.LD.add(hap.trans.pere,hap.trans.mere,perf,CD,map,position,

temps.depart,perfectLD,marq.hap.left)

hapim.LD.add