R help - Sep 2010 - Converting tables to matrices

Hi there,
I'm a real beginner to R. I have two tables of the following format (~1000
rows in each):
Table 1 (experimental)
N        bp
1064   12312089
856     12312234
....

Table 2 (control)
8463    34728908
879      34443290
.....

I would like to do Fisher's exact tests comparing each row of the tables
e.g. the test for row 1 would look something like this:
     Experimental    Control
N    1064              8463
bp  12312089        34728908

How do I either:
a) Create ~1000 2x2 matrices from each row of the two tables?, or
b) Use the fisher.test function repeatedly for each row of the two tables?

Thanks for our help!
Selthy
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Hello Selthy,

Here's one way. Assume your tables are called x.trt and x.cont

# form a single matrix
x <- cbind(x.trt, x.cont)
colnames(x) <- c("Ntrt", "BPtrt", "Ncon",
"BPcon")
result <- apply( x, 1, function(xrow) fisher.test( matrix(xrow, nrow=2) ) )

Now result is a list where element i holds the test results for row i
of your data. E.g. to get the results for row 1..

results[[1]]

Michael


On 17 September 2010 14:04, selthy <selthy at hotmail.com>
wrote:
>
> Hi there,
> I'm a real beginner to R. I have two tables of the following format
(~1000
> rows in each):
> Table 1 (experimental)
> N ? ? ? ?bp
> 1064 ? 12312089
> 856 ? ? 12312234
> ....
>
> Table 2 (control)
> 8463 ? ?34728908
> 879 ? ? ?34443290
> .....
>
> I would like to do Fisher's exact tests comparing each row of the
tables
> e.g. the test for row 1 would look something like this:
> ? ? Experimental ? ?Control
> N ? ?1064 ? ? ? ? ? ? ?8463
> bp ?12312089 ? ? ? ?34728908
>
> How do I either:
> a) Create ~1000 2x2 matrices from each row of the two tables?, or
> b) Use the fisher.test function repeatedly for each row of the two tables?
>
> Thanks for our help!
> Selthy
> --
> View this message in context:
http://r.789695.n4.nabble.com/Converting-tables-to-matrices-tp2543309p2543309.html
> Sent from the R help mailing list archive at Nabble.com.
>
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>