[R] Comparing two matrices

[Peter Dalgaard]

Srinivas Iyyer <srini_iyyer_bio at yahoo.com> writes:

> 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
> + }

There are much faster ways. Try (untested)

n1 <- match(tb$V1, rownames(tmat))
n2 <- match(tb$V2, colnames(tmat))
m <- unique(cbind(n1,n2)[complete.cases(n1,n2),])
tmat[m] <- 1

The unique() part may or may not be beneficial. 



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   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
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