| infer.haplos.cc {SimHap} | R Documentation |
infer.haplos.cc generates a haplotype object to be used in association analysis.
infer.haplos.cc(geno, pheno, cc.var)
geno |
a genotype data frame where each SNP is represented by two columns, one for each allele, in the form of haplo.dat. |
pheno |
a data frame containing phenotype data with at least two columns - a subject identifier and an indicator of disease status. |
cc.var |
the column name of the parameter indicating disease status. Must be entered with quotations, e.g. ``DISEASE". |
cc.var must be binary, taking only values 0 or 1.
infer.haplos.cc returns a list containing the following items
hapMat |
a dataframe containing all possible haplotype configurations with their respective likelihoods, for each individual. |
hap.freq.cases |
haplotype frequencies among cases estimated using the EM algorithm, and the standard errors of these frequencies. |
hap.freq.controls |
haplotype frequencies among controls estimated using the EM algorithm, and the standard errors of these frequencies. |
init.freq.cases |
initial haplotype frequencies among cases to be used by other SimHap functions. |
init.freq.controls |
initial haplotype frequencies among controls to be used by other SimHap functions. |
infer.haplos.cc is to be used in place of infer.haplos when haplotypes and haplotype frequencies are to be inferred independently in cases and controls. geno and pheno should have individuals in the same order, with the subject identifier column in ascending order.
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.
Stram, D.O., Leigh Pearce, C., Bretsky, P., Freedman, M., Hirschhorn, J.N., Altshuler, D., Kolonel, L.N., Henderson, B.E., Thomas, D.C. (2003) Modeling and EM Estimation of Haplotype-Specific Relative Risks from Genotype Data for a Case-Control Study of Unrelated Individuals, Human Heredity, 55:179-190.
data(SNP.dat)
# convert SNP.dat to format required by infer.haplos
haplo.dat <- SNP2Haplo(SNP.dat)
data(pheno.dat)
newdata <- prepare.cc(geno=haplo.dat, pheno=pheno.dat, cc.var="DISEASE")
newhaplo.dat <- newdata$geno
newpheno.dat <- newdata$pheno
# generates haplotype frequencies and haplotype design matrix
myinfer<-infer.haplos.cc(geno=newhaplo.dat,
pheno=newpheno.dat, cc.var="DISEASE")
# prints haplotype frequencies among cases
myinfer$hap.freq.cases
# prints haplotype frequencies among controls
myinfer$hap.freq.controls
# generated 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=newpheno.dat, haplo=myhaplo, sim=10)