prepare.cc {SimHap} | R Documentation |
prepare.cc
prepares case-control data when there may be missing values in the `case status' variable. This eliminates problems when using infer.haplos.cc
.
prepare.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". |
prepare.cc
searches for missing values in cc.var
and reduces geno
and pheno
to include only those individuals with known disease status. These geno
and pheno
objects can then be passed into infer.haplos.cc
.
geno |
a genotype data frame where each SNP is represented by two columns, one for each allele, in the form of haplo.dat . Individuals with unknown disease status are removed. |
pheno |
a data frame containing phenotype data with at least two columns - a subject identifier and an indicator of disease status. Individuals with unknown disease status are removed. |
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.cc haplo.dat <- SNP2Haplo(SNP.dat) data(pheno.dat) # not run: will return an error due to missing data in variable 'DISEASE' # myinfer<-infer.haplos.cc(geno=haplo.dat, pheno=pheno.dat, # cc.var="DISEASE") newdata <- prepare.cc(geno=haplo.dat, pheno=pheno.dat, cc.var="DISEASE") newhaplo.dat <- newdata$geno newpheno.dat <- newdata$pheno 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.bin(formula1=DISEASE~AGE+SBP+h.N1AA, formula2=DISEASE~AGE+SBP, pheno=newpheno.dat, haplo=myhaplo, sim=10)