Could you provide an example of mat1 and mat2 as well as an example of the
output you would like from them.

Your code is very difficult to follow as written.  It will be easier for
readers of the list to interpret if you use carriage returns rather than
semi colons, for example ...

fish <- function(x, y) {
n00 = sum((1-x)*(1-y))
n01 = sum((1-x)*y)
n10 = sum(x*(1-y))
 n11 = sum(x*y)
a = matrix(c(n00, n01, n10, n11), nrow=2)
pval = fisher.test(a)$p.value
 return(pval)
}

Jean


On Mon, Jun 24, 2013 at 6:09 AM, Angel Russo <angerusso1980@gmail.com>wrote:

> **
>
> I am using the following way to get p-values from fiser exact test.
> However, I do need to print for each pair the values "n00, n01, n10, n11".
> How can I print that as a table and not a matrix as below along with the
> p-value? Any help will be greatly appreciated
>
>  fish <- function(y, x) {n00 = sum((1-x)*(1-y)); n01 = sum((1-x)*y);
> n10 = sum(x*(1-y)); n11 = sum(x*y); a = matrix(c(n00, n01, n10, n11),
> nrow = 2); pval = fisher.test(a)$p.value; return(pval);}
>
>  chiArray <- function(x) {  apply(mat1, 1, fish, x); }
>  sapply(1:nrow(mat2), function(j){chiArray(mat2[j, ]);});
>  chisq.cna.mut.test <- sapply(1:nrow(mat2), function(j){chiArray(mat2[j,
> ]);});
>
> I want output to be:
>
> name1_mat1 name1_mat2 n00 n01 n10 n11 pvalue
>
>
>
> name1_mat1 name2_mat2 n00 n01 n10 n11 pvalue
>
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