infer.haplos {SimHap}R Documentation

Infer haplotype configurations when phase is unknown

Description

infer.haplos generates a haplotype object to be used in association analysis.

Usage

infer.haplos(geno)

Arguments

geno a genotype data frame where each SNP is represented by two columns, one for each allele, in the form of haplo.dat

Value

infer.haplos returns a list containing the following items

hapMat a dataframe containing all possible haplotype configurations with their respective likelihoods, for each individual.
hap.freq haplotype frequencies estimated using the EM algorithm, and the standard errors of these frequencies.
initFreq initial haplotype frequencies to be used by other SimHap functions.

Author(s)

Pamela A. McCaskie

References

Excoffier, L., Slatkin, M.. (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular Biology Evolution, 12(5):921-927.

McCaskie, P.A., Carter, K.W, Hazelton, M., Palmer, L.J. (2007) SimHap: A comprehensive modeling framework for epidemiological outcomes and a multiple imputation approach to haplotypic analysis of population-based data, [online] www.genepi.org.au/simhap.

See Also

make.haplo.rare

Examples


data(SNP.dat)

# convert SNP.dat to format required by infer.haplos
haplo.dat <- SNP2Haplo(SNP.dat)

data(pheno.dat)

# generates haplotype frequencies and haplotype design matrix
myinfer<-infer.haplos(haplo.dat) 

# prints haplotype frequencies generated by infer.haplos
myinfer$hap.freq 

# generates haplo object where haplotypes with a frequency 
# below min.freq are grouped as a category called "rare"
myhaplo<-make.haplo.rare(myinfer,min.freq=0.05) 
mymodel <- haplo.quant(formula1=HDL~AGE+SBP+h.N1AA, formula2=HDL~AGE+SBP, 
        pheno=pheno.dat, haplo=myhaplo, sim=10)


[Package SimHap version 1.0.0 Index]