| infer.haplos {SimHap} | R Documentation |
infer.haplos generates a haplotype object to be used in association analysis.
infer.haplos(geno)
geno |
a genotype data frame where each SNP is represented by two columns, one for each allele, in the form of haplo.dat |
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. |
Pamela A. McCaskie
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.
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)