R help - Sep 2009 - Best way to arrange data

Hello,
I have the following data:

   gene Actual    groups    reps
1    1    213         1            2
2    2    123         2            3
3    3       2         1            2
4    4     12          2           3
5    1       0          1           1
6    2     34          2           2
7    3    123         1           1
8    4      12         2           2

I want to find the best way to store this so that it can be accessed quickly
for other uses. Someone recommended an array as follows:



actual_array=array(0,c(G,T,length(nj)))
for (b in 1:length(gene)) {
     for (i in 1:max(gene))  {
         for (j in 1:max(groups))  {
              for (k in 1:max(reps)) {
                  if ((gene[b]==i) && (groups[b]==j) &&
(replicate[b]==k))
                     {
                         yijk_array[i,j,k]=yijk[b]
                     }
                                            }
                                          }
                                    }
                                 }


But this gives an array that has a lot of zeros in places where I don't have
any data. Is there a way to overcome this and present a 'shortened'
version?


Jim

	[[alternative HTML version deleted]]

On Sep 23, 2009, at 3:47 PM, Jim Silverton wrote:
> Hello,
> I have the following data:
>
>   gene Actual    groups    reps
> 1    1    213         1            2
> 2    2    123         2            3
> 3    3       2         1            2
> 4    4     12          2           3
> 5    1       0          1           1
> 6    2     34          2           2
> 7    3    123         1           1
> 8    4      12         2           2
>
> I want to find the best way to store this so that it can be accessed  
> quickly
> for other uses. Someone recommended an array as follows:
>
>
>
> actual_array=array(0,c(G,T,length(nj)))
> for (b in 1:length(gene)) {
>     for (i in 1:max(gene))  {
>         for (j in 1:max(groups))  {
>              for (k in 1:max(reps)) {
>                  if ((gene[b]==i) && (groups[b]==j) &&  
> (replicate[b]==k))
>                     {
>                         yijk_array[i,j,k]=yijk[b]
>                     }
>                                            }
>                                          }
>                                    }
>                                 }
>
>
> But this gives an array that has a lot of zeros in places where I  
> don't have
> any data. Is there a way to overcome this and present a 'shortened'
> version?

The Matrix package has a sparse array construct that may ffer what you  
seek.

-- 
David.
>
>
> Jim
>
> 	[[alternative HTML version deleted]]
>
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Heritage Laboratories
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