make.haplo.rare {SimHap} | R Documentation |
make.haplo.rare
groups haplotypes with frequencies below a specified threshold together and processes data into a format compatible with the haplotype analysis functions
make.haplo.rare(infer.object, min.freq)
infer.object |
result of a call to infer.haplos . |
min.freq |
minimum frequency of haplotypes to include in analysis. Haplotype with a frequency below this value will be grouped together in a group called `rare'. |
hapData |
A data frame containing all haplotype configurations and their posterior probabilities for each individual, grouping rare haplotypes into a category called `rare'. |
hapObject |
A list containing the original haplotype information for each individual as well as haplotype frequency tables |
Pamela A. McCaskie
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) # generate haplotype frequencies and haplotype design matrix myinfer<-infer.haplos(haplo.dat) # print haplotype frequencies generated by infer.haplos myinfer$hap.freq # generate 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)