When sharing data, use dput() to output the data in a way that R-Help
readers can easily use.

Give this code a try and see if it helps.

Jean



# read in the example data
mat1 <- structure(list("GENE SYMBOL" = c("ADCK2", "ADCK3", "ADCK4",
"ADCK5",
 "ADRBK1", "ADRBK2", "AKT1", "AKT2", "AKT3", "ALK"), Sample.A1.A0SK.01 =
c(0L,
0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A1.A0SO.01 = c(0L,
 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A1.A0SP.01 = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A04P.01 = c(0L,
 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A04Q.01 = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A04U.01 = c(0L,
 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L), Sample.A2.A0CL.01 = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A0CM.01 = c(0L,
 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A0D0.01 = c(0L,
1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L), Sample.A2.A0D2.01 = c(1L,
 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A0ST.01 = c(0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), Sample.A2.A0SX.01 = c(0L,
 1L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 0L), Sample.A2.A0T0.01 = c(0L,
0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L)), .Names = c("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"), class = "data.frame", row.names = c(NA, -10L))
mat2 <- mat1

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(c(n00, n01, n10, n11, pval))
}

results <- data.frame(matrix(NA, nrow=dim(mat1)[1]*dim(mat2)[1], ncol=7,
dimnames=list(NULL, c("gene1", "gene2", "n00", "n01", "n10", "n11",
"pval"))))
count <- 0
for(i in 1:dim(mat1)[1]) {
for(j in 1:dim(mat2)[1]) {
count <- count + 1
results[count, "gene1"] <- mat1$"GENE SYMBOL"[i]
 results[count, "gene2"] <- mat2$"GENE SYMBOL"[j]
results[count, 3:7] <- fish(mat1[i, -1], mat2[j, -1])
 }}



On Mon, Jun 24, 2013 at 10:35 AM, Angel Russo <angerusso1980@gmail.com>wrote:

> 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 <jvadams@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)$p.value
>>  return(pval)
>> }
>>
>> Jean
>>
>>
>> On Mon, Jun 24, 2013 at 6:09 AM, Angel Russo <angerusso1980@gmail.com>wrote:
>>
>>> **
>>>
>>> I am using the following way to get p-values from fiser exact test.
>>> However, I do need to print for each pair the values "n00, n01, n10,
>>> n11".
>>> How can I print that as a table and not a matrix as below along with the
>>> p-value? Any help will be greatly appreciated
>>>
>>>  fish <- function(y, x) {n00 = sum((1-x)*(1-y)); n01 = sum((1-x)*y);
>>> n10 = sum(x*(1-y)); n11 = sum(x*y); a = matrix(c(n00, n01, n10, n11),
>>> nrow = 2); pval = fisher.test(a)$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
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>

	[[alternative HTML version deleted]]

