R help - May 2002 - Fisher test

Hello! I started from two matrix. I made "margin.table" and so now I
have
two vectors. I have to take the first elements of the two vectors, and the
sum of the remaining element of each vector.
I make a example.Suppose to have (1,3,5,7,9)
                                 (2,6,8,0,1)
I want to take 1,2 that are the first elements of the vectors, and make
3+5+7+9=24 for the first vector and 6+8+0+1=15 for the second. At this point
I build a table in this way
   1  24
   2  15
For this table I use the Fisher exact test. After this I have to take the
second elements of the vectors, find the sum of the rest of the vectors,
build another table and make Fisher. I have to do it for all the elements of
the vectors. In this case I have to find 5 tables. The problem is that I
have vectors with 1000 elements.
I know that I have to use "for" to build the table.
I know also that everytime fisher.test gives me the reslut.
The question is: have I to see one by one all the 1000 results or is there a
way to  create for example  a table with all the p-values or all the
confidence intervals? At the end my object is to say for example that 700
tables rejected the null hypothesis and 300 no.
Plese help me.
Thank you
Alessandro

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On Thu, 30 May 2002, Ambrosini Alessandro wrote:
> Hello! I started from two matrix. I made "margin.table" and so
now I have
> two vectors. I have to take the first elements of the two vectors, and the
> sum of the remaining element of each vector.
> I make a example.Suppose to have (1,3,5,7,9)
>                                  (2,6,8,0,1)
> I want to take 1,2 that are the first elements of the vectors, and make
> 3+5+7+9=24 for the first vector and 6+8+0+1=15 for the second. At this
point
> I build a table in this way
>    1  24
>    2  15
> For this table I use the Fisher exact test. After this I have to take the
> second elements of the vectors, find the sum of the rest of the vectors,
> build another table and make Fisher. I have to do it for all the elements
of
> the vectors. In this case I have to find 5 tables. The problem is that I
> have vectors with 1000 elements.
> I know that I have to use "for" to build the table.
> I know also that everytime fisher.test gives me the reslut.
Suppose a and b are your two vectors.  You can do

A<-rev(cumsum(rev(a))
B<-rev(cumsum(rev(b))

and then
   pvalues<-sapply(1:999, function(i)
   	fisher.test(matrix(c(a[i],b[i],A[i+1],B[i+1]),2))$p.values)
using the fact (which you can discover from the help or by using str())
that the p value is the $p.value component of the result of the test.

You could also construct a 2x2x999 array from a[-1000],b[-1000],A[-1] and
B[-1] and use apply() to do the tests to each layer
   M<-array(c(a[-1000],b[-1000],A[-1],B[-1]),dim=c(999,2,2))
   pvalues<-apply(M,1,function(m) fisher.test(m)$p.value)

or use a for() loop explicitly, in which case you need to define the
vector first

pvalues<-numeric(999)
for(i in 1:999){
   pvalues[i]<- fisher.test(matrix(c(a[i],b[i],A[i+1],B[i+1]),2))$p.values
}

I think the apply version is the neatest.  They all seem to have about the
same speed on the one example I tried.


	-thomas

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