Dear all,

I have a data frame 144 x 20000 values.
I need to take every value in the first row and compare to the second row,
and the same for rows 3-4 and 5-6 and so on.
the output should be one line for each of the two row comparison.
the comparison is:
if row1==1 and row2==1 <-'HT'
if row1==1 and row2==0 <-'A'
if row1==0 and row2==1 <-'B'
if row1==1 and row2=='-' <-'Aht'
if row1=='-' and row2==1 <-'Bht'

for example:
if the data is:
CloneID    genotype 2001    genotype 2002    genotype 2003
2471250    1    1    1
2471250    0    0    0
2433062    0    0    0
2433062    1    1    1
100021605    1    1    0
100021605    1    0    1
100005599    1    1    0
100005599    1    1    1
100002798    1    1    0
100002798    1    1    1

then the output should be:
CloneID    genotype 2001    genotype 2002    genotype 2003
2471250    A    A    A
2433062    B    B    B
100021605    HT    A    B
100005599    HT    HT    B
100002798    HT    HT    B

I tried this for the whole data, but its so slow:

AX <- data.frame(lapply(AX, as.character), stringsAsFactors=FALSE)


for (i in seq(1,nrow(AX),by=2)){
for (j in 6:144){
if (AX[i,j]==1 & AX[i+1,j]==0){
AX[i,j]<-'A'
}
if (AX[i,j]==0 & AX[i+1,j]==1){
AX[i,j]<-'B'
}
if (AX[i,j]==1 & AX[i+1,j]==1){
AX[i,j]<-'HT'
}
if (AX[i,j]==1 & AX[i+1,j]=="-"){
AX[i,j]<-'Aht'
}
if (AX[i,j]=="-" & AX[i+1,j]==1){
AX[i,j]<-'Bht'
}
}
}

AX1<-AX[!duplicated(AX[,3]),]
AX2<-AX[duplicated(AX[,3]),]

Thanks for any help,

Raz



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