hapim.LD.add: HAPimLD method
In HAPim: HapIM

Description Usage Arguments Details Value Author(s) References Examples

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.

1
2
3

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

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

`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.

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.

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

S. Dejean, N. Oumouhou, D. Estivals, B. Mangin

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.

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