haplomax.add: HaploMax method in unrelated population

Description Usage Arguments Details Value Author(s) References Examples

Description

The function computes an analysis of variance with a dose haplotype effect.

Usage

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haplomax.add(hap.trans.pere, hap.trans.mere, perf, CD, map, marq.hap)

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.

marq.hap

number of markers of the mutated haplotype

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.

Test positions are located on the middles of marq.hap marker sliding windows.

Value

The value returned is a data frame which contains 5 columns:

-Test positions

-Value of Fisher test

-Mutated (i.e. associated to Q allele) haplotype

-Estimate of the error variance

-Estimate of the Q allele effect

Author(s)

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

References

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

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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 use a 2 markers-associated haplotype.
marq.hap=2

haplomax=haplomax.add(hap.trans.pere,hap.trans.mere,perf,CD,map, marq.hap)

haplomax

HAPim documentation built on May 30, 2017, 3:13 a.m.