From: Srinivas Iyyer <srini_iyyer_bio_at_yahoo.com>

Date: Sat 29 Jul 2006 - 06:21:01 EST

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R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sat Jul 29 06:24:59 2006

Date: Sat 29 Jul 2006 - 06:21:01 EST

Hi Andy, Thank you very much for your previous tip.

However, I am running into another problem now.

previously, in my tab-delim file I had only two columns. now I added another column. and I want the pairs value to go into the matrix instead of 1. pair (Apple, S) value 10.

*> > > tb # tab- delim file.
**> > V1 V2 V3
**> > 1 Apple S 10
**> > 2 Apple A 12
**> > 3 Apple O 34
**> > 4 Orange A 34
**> > 5 Orange O 59
**> > 6 Orange S 30
**> > 7 Mango M 395
*

> > 8 Mango A 495

> > 9 Mango S 302

Now I am trying to do the following:

R> tbm <- as.matrix(tb) # turn it into a character
matrix

R> tmat[cbind(match(tbm[,2],

rownames(tmat)),match(tbm[,1],colnames(tmat)))] <-
tbm[,3]

Error: NAs are not allowed in subscripted assignments

I get the above error.

What is wrong with this. I am using R.2.2.1 on a Dell Latutite windows XP with 1GB RAM.

Could any one please help me what am I doing wrong.

thank you.

- "Liaw, Andy" <andy_liaw@merck.com> wrote:

> It might be a bit faster to do matrix indexing:

*>
**> R> tbm <- as.matrix(tb) # turn it into a character
**> matrix
**> R> tmat[cbind(match(tbm[,2], rownames(tmat)),
**> match(tbm[,1],
**> colnames(tmat)))] <- 1
**> > tmat
**> Apple Orange Mango Grape Star
**> A 1 1 1 0 0
**> O 1 1 0 0 0
**> M 0 0 1 0 0
**> G 0 0 0 0 0
**> S 1 1 1 0 0
**>
**> HTH,
**> Andy
**>
**>
**> From: Srinivas Iyyer
**> >
**> > hi:
**> >
**> > I have matrix with dimensions(200 X 20,000). I
**> have another
**> > file, a tab-delim file where first column
**> variables are row
**> > names and second column variables are column
**> names.
**> >
**> >
**> > For instance:
**> >
**> > > tmat
**> > Apple Orange Mango Grape Star
**> > A 0 0 0 0 0
**> > O 0 0 0 0 0
**> > M 0 0 0 0 0
**> > G 0 0 0 0 0
**> > S 0 0 0 0 0
**> >
**> >
**> >
**> > > tb # tab- delim file.
**> > V1 V2
**> > 1 Apple S
**> > 2 Apple A
**> > 3 Apple O
**> > 4 Orange A
**> > 5 Orange O
**> > 6 Orange S
**> > 7 Mango M
**> > 8 Mango A
**> > 9 Mango S
**> >
**> >
**> > I have to read each line of the 'tb' (tab delim
**> file), take
**> > the first variable, check if matches any rowname
**> of the
**> > matrix. Take the second variable of the row in and
**> check if
**> > it matches any column name. If so, put
**> > 1 else leave it.
**> >
**> >
**> > The following is a small piece of code that, I
**> felt is a
**> > solutions. However, since my original matrix and
**> tab-delim
**> > file is very very huge, I am not sure if it is
**> really doing
**> > the correct thing. Could any one please help me if
**> I am doing
**> > this correct.
**> >
**> >
**> >
**> > > for(i in 1:length(tb[,1])){
**> > + r = tb[i,1]
**> > + c = as.character(tb[i,2])
**> > + tmat[rownames(tmat)==c,colnames(tmat)==r] <-1 }
**> >
**> >
**> >
**> > > tmat
**> > Apple Orange Mango Grape Star
**> > A 1 1 1 0 0
**> > O 1 1 0 0 0
**> > M 0 0 1 0 0
**> > G 0 0 0 0 0
**> > S 1 1 1 0 0
**> >
**> >
**> >
**> > Thanks.
**> >
**> > ______________________________________________
**> > R-help@stat.math.ethz.ch mailing list
**> > https://stat.ethz.ch/mailman/listinfo/r-help
**> > PLEASE do read the posting guide!
**> > http://www.R-project.org/posting-guide.html
**> >
**> >
**>
**>
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R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sat Jul 29 06:24:59 2006

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