---------- Forwarded message ---------- From: Dr. Venkatesh <drve...@liv.ac.uk> Date: Sun, May 9, 2010 at 4:55 AM Subject: R apply() help -urgent To: r-help@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!! ♪
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