setwd("C:/Zkristel 1jan2010/Courses/Courses Liege My Own/Class Liege 2009-2010/Genetic Epi 2010/Public Health Epi/Final Version of the Chapters/cursusdata2010")

#ped file with header
pedigree2.ped <- read.table(file="pedigree2.ped",header=FALSE,sep=" ")
nr.of.allele.columns <- length(names(pedigree2.ped[,7:ncol(pedigree2.ped)]))
marker.nrs <- 1: (nr.of.allele.columns /2)
names <- paste("SNP",sort(rep(marker.nrs,2)),c("a","b"),sep="")
names(pedigree2.ped) <- c("PID","ID","FID","MID","sex","status",names)
write.table(pedigree2.ped,file="pedigree.ped",col.names=TRUE,row.names=FALSE,sep=" ",quote=FALSE)

#phe file with header
pedigree.phe <- read.table(file="pheno.dat",header=TRUE, sep=" ")