[R] Comparing two matrices

From: Srinivas Iyyer <srini_iyyer_bio_at_yahoo.com>
Date: Thu 06 Jul 2006 - 22:18:47 EST


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.



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