Hello, Raz,
if X is the data frame that contains your data, then using sort of an
"indexing trick" to circumvent your numerous if-statements as in
aggregate( X[ c( "genotype 2001", "genotype 2002", "genotype 2003")],
X[ "CloneID"],
FUN = function( x)
c( "11" = "HT",
"10" = "A",
"01" = "B",
"1-" = "Aht",
"-1" = "Bht")[ paste( x, collapse = "")])
presumably does what you want (and can certainly be improved).
Hth -- Gerrit
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On Mon, 4 Aug 2014, raz wrote:
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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