On May 9, 2010, at 12:30 AM, Venkatesh Patel wrote:
---------- 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
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
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to kill ♬ Who knows what miracles you can achieve when you believe
♪♬
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--
♪ 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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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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