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

[Venkatesh Patel]

---------- 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
P      5   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
F      6   0   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     1
E      4   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
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
J      4   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0
  0   0   0   0   0   0   0   0   0     1
J      4   0   0   0   0   0   0   0   0   0   1   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
S      6   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
  0   1   0   0   0   0   0   0   0     1
..
..
..
..
..
..

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.

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!! ♪