[R] numeric(0)
BXC (Bendix Carstensen)
bxc at steno.dk
Wed Dec 29 14:47:29 CET 2004
You would probably be better off without the loop, for example:
ns <- length( sequence )
num.seq <- match( sequence, names )
scores <- mscore[cbind(num.seq[-1],num.seq[-ns])]
sum( scores )
I have used the fact that if you index a matrix with
a two-column,matrix ( here, cbind( , ) ), you select the
corresponding elements of the matrix, see ?"["
But it only works if the matrix is numeric.
Bendix Carstensen
----------------------
Bendix Carstensen
Senior Statistician
Steno Diabetes Center
Niels Steensens Vej 2
DK-2820 Gentofte
Denmark
tel: +45 44 43 87 38
mob: +45 30 75 87 38
fax: +45 44 43 07 06
bxc at steno.dk
www.biostat.ku.dk/~bxc
----------------------
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of dax42
> Sent: Wednesday, December 29, 2004 2:18 PM
> To: r-help at stat.math.ethz.ch
> Subject: [R] numeric(0)
>
>
> Dear all,
>
> I am trying to calculate a score for a string sequence consisting of
> the following four letters: ACGT.
> I have got a matrix giving the scores for each pair of
> letters. So for example the string ACCT has got the pairs:
> AC, CC and CT.
>
> The matrix has got the following form:
> names<-c("A","C","G","T"); mscore<-matrix(0,4,4);
> rownames(mscore)<-names; colnames(mscore)<-names;
>
> So for the first example pair above I could get the score
> contained in
> the matrix with the following code:
> >> mscore["A","C"]
>
> I am now trying to sum up all the scores with the following code:
>
> score<-0;
>
> for(j in 1:length(sequence)-1){
> score<-score+mscore[sequence[j],sequence[j+1]];
> }
>
> where sequence is the string sequence.
> Unfortunately, it does not work and I get the following error message:
>
> Error in "[<-"(`*tmp*`, 1, i, value = numeric(0)) :
> nothing to replace with
>
> What does this mean? Strangely, the command
> "print(score+mscore[sequence[j],sequence[j+1]])"
> works, so it really is the assignment which won't work. Why
> is that? I am running R 2.0 series (GUI version) on Mac OSX 10.3.7.
>
> Any suggestions are welcome.
> Thanks a lot,
> Dax
>
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