help needed with printing multiple arguments as vectors, not matrices

Sample data is as follows (for simplicity assume mat1 and mat2 are the same
matrices). Also attached as an excel file.

I want to get the pairwise interaction fischer test results. Not just the
pvalues but also want to wrote the n00, n01, n10 and n11 in the file as:


ADCK2_mat1 ADCK3_mat2 n00 n01 n10 n11 pvalue



ADCK2_mat1 ADCK4_mat2 n00 n01 n10 n11 pvalue

 GENE SYMBOL Sample-A1-A0SK-01 Sample-A1-A0SO-01 Sample-A1-A0SP-01
Sample-A2-A04P-01 Sample-A2-A04Q-01 Sample-A2-A04U-01 Sample-A2-A0CL-01
Sample-A2-A0CM-01 Sample-A2-A0D0-01 Sample-A2-A0D2-01 Sample-A2-A0ST-01
Sample-A2-A0SX-01 Sample-A2-A0T0-01  ADCK2 0 0 0 0 0 0 0 0 0 1 0 0 0  ADCK3
0 0 0 0 0 1 0 0 1 0 0 1 0  ADCK4 0 0 0 0 0 0 0 0 0 0 0 1 0  ADCK5 1 0 0 0 0
0 0 0 0 0 0 0 1  ADRBK1 0 0 0 0 0 0 0 0 0 0 0 0 0  ADRBK2 0 0 0 0 0 1 0 0 0
0 0 0 0  AKT1 0 0 0 0 0 0 0 0 0 0 0 0 0  AKT2 0 0 0 0 0 0 0 0 0 0 0 1 0
AKT3 0 0 0 0 0 0 0 0 1 0 0 1 0  ALK 0 0 0 0 0 0 0 0 0 0 0 0 0

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 at 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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-------------- next part --------------
GENE SYMBOL	Sample-A1-A0SK-01	Sample-A1-A0SO-01	Sample-A1-A0SP-01	Sample-A2-A04P-01	Sample-A2-A04Q-01	Sample-A2-A04U-01	Sample-A2-A0CL-01	Sample-A2-A0CM-01	Sample-A2-A0D0-01	Sample-A2-A0D2-01	Sample-A2-A0ST-01	Sample-A2-A0SX-01	Sample-A2-A0T0-01
ADCK2	0	0	0	0	0	0	0	0	0	1	0	0	0
ADCK3	0	0	0	0	0	1	0	0	1	0	0	1	0
ADCK4	0	0	0	0	0	0	0	0	0	0	0	1	0
ADCK5	1	0	0	0	0	0	0	0	0	0	0	0	1
ADRBK1	0	0	0	0	0	0	0	0	0	0	0	0	0
ADRBK2	0	0	0	0	0	1	0	0	0	0	0	0	0
AKT1	0	0	0	0	0	0	0	0	0	0	0	0	0
AKT2	0	0	0	0	0	0	0	0	0	0	0	1	0
AKT3	0	0	0	0	0	0	0	0	1	0	0	1	0
ALK	0	0	0	0	0	0	0	0	0	0	0	0	0