Set up a function for the fisher.test on a 2x2 table and then include
this in the apply function for columns as in the example below. The
result is a list with names A to Z
# set up a dummy data set with 100 rows
Cat<-LETTERS[sample(1:6,100, replace=T)]
GL<-sample(1:6, 100, replace=T)
dat<-matrix(sample(c(0,1),100*27, replace=T), nrow=100)
colnames(dat)<-c(LETTERS[1:26],"pLoss")
data1<-data.frame(Cat, GL, dat)
# define function fro fisher.test
ff<-function(x,y){
fisher.test(table(x,y))
}
# apply function to columns A to Z
results<-apply(data1[,LETTERS[1:26]],2, ff, y=data1[,"pLoss"])
# the results are in the form of a list with names A to Z
results$C
On 19:59, Venkatesh Patel wrote:
---------- Forwarded message ----------
From: Dr. Venkatesh<drve...@liv.ac.uk>
Date: Sun, May 9, 2010 at 4:55 AM
Subject: R apply() help -urgent
To: r-help@r-project.org
I have a file with 4873 rows of 1s or 0s and has 26 alphabets (A-Z) as
columns. the 27th column also has 1s and 0s but stands for a different
variable (pLoss). columns 1 and 2 are not significant and hence lets ignore
them for now.
here is how the file looks
Cat GL A B C D E F G H I J K L M N O P Q
R S T U V W X Y Z pLoss
H 5 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
E 5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
P 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 1
P 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 1
F 6 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
E 4 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
H 5 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
J 4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
J 4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
E 5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1
S 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 0 0 0 0 0 0 0 1
..
..
..
..
..
..
Alphabets A-Z stand for different categories of protein families and pLoss
stands for their presence or absence in an animal.
I intend to do Fisher's test for 26 individual 2X2 tables constructed from
each of these alphabets vs pLoss.
For example, here is what I did for alphabet A and then B and then C.... so
on. (I have attached R-input.csv for your perusal)
data1<- read.table("R_input.csv", header = T)
datatable<- table(data1$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
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