[R] Fwd: R apply() help -urgent

[David Winsemius]

On May 9, 2010, at 12:30 AM, Venkatesh Patel wrote:

> ---------- Forwarded message ----------
> From: Dr. Venkatesh <drvenki at liv.ac.uk>
> Date: Sun, May 9, 2010 at 4:55 AM
> Subject: R apply() help -urgent
> To: r-help at r-project.org
>
>
> I have a file with 4873 rows of 1s or 0s and has 26 alphabets (A-Z) as
> columns. the 27th column also has 1s and 0s but stands for a different
> variable (pLoss). columns 1 and 2 are not significant and hence lets  
> ignore
> them for now.
>
> here is how the file looks
>
> Cat    GL  A   B   C   D   E   F   G   H   I   J   K   L   M   N    
> O   P   Q
>  R   S   T   U   V   W   X   Y   Z     pLoss
> H      5   0   0   0   0   0   0   0   1   0   0   0   0   0   0    
> 0   0   0
>  0   0   0   0   0   0   0   0   0     1
> E      5   0   0   0   0   1   0   0   0   0   0   0   0   0   0    
> 0   0   0
>  0   0   0   0   0   0   0   0   0     1
> P      6   0   0   0   0   0   0   0   0   0   0   0   0   0   0    
> 0   1   0
>  0   0   0   0   0   0   0   0   0     1
> snipped
> ..
> ..

> Alphabets A-Z stand for different categories of protein families and  
> pLoss
> stands for their presence or absence in an animal.
>
> I intend to do Fisher's test for 26 individual 2X2 tables  
> constructed from
> each of these alphabets vs pLoss.
>
> For example, here is what I did for alphabet A and then B and then  
> C.... so
> on. (I have attached R-input.csv for your perusal)
>
>> data1 <- read.table("R_input.csv", header = T)
>> datatable <- table(data1$A, data1$pLoss) #create a new datatable2  
>> or 3
> with table(data1$B.. or  (data1$C.. and so on
>> datatable
>
>       0    1
>  0   31 4821
>  1    0   21
>
> now run the Fisher's test for these datatables one by one for the 26
> alphabets :(
>
> fisher.test(datatable), ... fisher.test(datatable2)...
>
> in this case, the task is just for 26 columns.. so I can do it  
> manually.
>
> But I would like to do an automated extraction and fisher's test for  
> all the
> columns.

  tbl.list <- apply(dfrm[, 3:29] , 2, function(x) table(x, dfrm$pLoss))
  lapply(tbl.list, function(x) if (nrow(x) >1 && ncol(x) >1)  
fisher.test(x))

>
> I tried reading the tutorials and trying a few examples. Cant really  
> come up
> with anything sensible.
>
> How can I use apply() in this regard? or is there any other way, a  
> loop may
> be? to solve this issue.
>
> Please help.
>
> Thanks a million in advance,
>
> Dr Venkatesh Patel
> School of Biological Sciences
> University of Liverpool
> United Kingdom
>
>
> -- 
> ♪ There can be miracles when you believe ♪♬ Though hope is  
> frail, it's hard
> to kill ♬ Who knows what miracles you can achieve when you believe  
> ♪♬
> Somehow you will.. when you believe!! ♪
>
>
>
> -- 
> ♪ There can be miracles when you believe ♪♬ Though hope is  
> frail, it's hard
> to kill ♬ Who knows what miracles you can achieve when you believe  
> ♪♬
> Somehow you will.. when you believe!! ♪
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David Winsemius, MD
West Hartford, CT