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
On Mon, Jun 24, 2013 at 11:03 AM, Adams, Jean <jvad...@usgs.gov> wrote:
> 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)$p.value
> return(pval)
> }
>
> Jean
>
>
> On Mon, Jun 24, 2013 at 6:09 AM, Angel Russo <angerusso1...@gmail.com>wrote:
>
>> **
>>
>> I am using the following way to get p-values from fiser exact test.
>> However, I do need to print for each pair the values "n00, n01, n10, n11".
>> How can I print that as a table and not a matrix as below along with the
>> p-value? Any help will be greatly appreciated
>>
>> fish <- function(y, x) {n00 = sum((1-x)*(1-y)); n01 = sum((1-x)*y);
>> n10 = sum(x*(1-y)); n11 = sum(x*y); a = matrix(c(n00, n01, n10, n11),
>> nrow = 2); pval = fisher.test(a)$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
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
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
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