[BioC] Random Matrices

[Matthew R. Helmus]

Hi Sean,
Thanks for your reply. I have a large data matrix (500x50) of values and 
I need to:
1) randomize
2) for each row apply a function
3) calculate the mean of the outputs of the function across the rows
4) store this mean
5) then repeat the loop 10,000 times to produce a vector of 10,000 
random means.

I have used the following code, apply(X, 1, sample), to make a 
randomized matrix maintaining row sums, but the for loop runs a bit slow 
that creates each random matrix. I have not developed or found code that 
maintains both row and sum totals while randomizing.

Thank in advance!
 Matt

Sean Davis wrote:
> On Thu, Apr 3, 2008 at 3:06 PM, Matthew R. Helmus <mrhelmus at wisc.edu> wrote:
>   
>> Hi,
>>  Does anyone know of an R function, code, or extension that makes and
>>  stores multiple randomizations of a data matrix quickly? Specifically, a
>>  function that maintains the sums of columns (samples), or rows (genes),
>>  or both. Those functions I have found are slow for large data matrices.
>>     
>
> Hi, Matt.
>
> You'll probably want to give us some code or at least more of a
> description of what you are trying to do.  That said, sample() is
> useful for doing resampling.  colSums() and rowSums() are optimized
> for just those computations.
>
> Sean
>