[R] Compare data in two rows and replace objects in data frame

[Gerrit Eichner]

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
>
>
>
> -- 
> \m/
>
> 	[[alternative HTML version deleted]]
>
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