[R] Comparing two matrices [Broadcast]

[Srinivas Iyyer]

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 at 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 at 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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