Nothing
tdt.cnt<-function(sample){
#Mother with genotype 1
idx.100=length(grep(TRUE, (sample[,2]==1&sample[,3]==0&sample[,4]==0)))
idx.101=length(grep(TRUE, (sample[,2]==1&sample[,3]==0&sample[,4]==1)))
idx.102=length(grep(TRUE, (sample[,2]==1&sample[,3]==0&sample[,4]==2)))
idx.110=length(grep(TRUE, (sample[,2]==1&sample[,3]==1&sample[,4]==0)))
idx.112=length(grep(TRUE, (sample[,2]==1&sample[,3]==1&sample[,4]==2)))
idx.120=length(grep(TRUE, (sample[,2]==1&sample[,3]==2&sample[,4]==0)))
idx.121=length(grep(TRUE, (sample[,2]==1&sample[,3]==2&sample[,4]==1)))
idx.122=length(grep(TRUE, (sample[,2]==1&sample[,3]==2&sample[,4]==2)))
#Father with genotype 1
idx.010=length(grep(TRUE, (sample[,3]==1&sample[,2]==0&sample[,4]==0)))
idx.011=length(grep(TRUE, (sample[,3]==1&sample[,2]==0&sample[,4]==1)))
idx.012=length(grep(TRUE, (sample[,3]==1&sample[,2]==0&sample[,4]==2)))
idx.210=length(grep(TRUE, (sample[,3]==1&sample[,2]==2&sample[,4]==0)))
idx.211=length(grep(TRUE, (sample[,3]==1&sample[,2]==2&sample[,4]==1)))
idx.212=length(grep(TRUE, (sample[,3]==1&sample[,2]==2&sample[,4]==2)))
if (dim(sample)[2]==5){
idx=sample[,5]
idx.111M=length(grep(TRUE, (sample[,2]==1&sample[,3]==1&sample[,4]==1&idx==1)))
idx.111F=length(grep(TRUE, (sample[,2]==1&sample[,3]==1&sample[,4]==1&idx==0)))
b.m=idx.101+idx.111M+idx.112+idx.122
c.m=idx.100+idx.110+idx.111F+idx.121
b.f=idx.111F+idx.112+idx.011+idx.212
c.f=idx.110+idx.111M+idx.010+idx.211
b=idx.101+idx.111M+idx.111F+2*idx.112+idx.122+idx.011+idx.212
c=idx.100+2*idx.110+idx.111M+idx.111F+idx.121+idx.010+idx.211
cnt=c(b.m,c.m,b.f,c.f,b,c)
} else if (dim(sample)[2]==4){
idx.111=length(grep(TRUE, (sample[,2]==1&sample[,3]==1&sample[,4]==1)))
b=idx.101+idx.111+2*idx.112+idx.122+idx.011+idx.212
c=idx.100+2*idx.110+idx.111+idx.121+idx.010+idx.211
cnt=c(NA,NA,NA,NA,b,c)
}
names(cnt)=c('b.m','c.m','b.f','c.f','b','c')
cnt
}
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