Question

I am trying do the Fisher Exact Test for more than 400 dates. The Fisher Exact Test works 2×2 possibilities. This test is to many used in molecular markers and genetics studies.
So, if I have to many dates, became impossible make all possibilities one to one combination of markers.

Analysis code in R:

alelo1<-data[,1]
alelo2<-data[,2]
fisher.test(alelo1,alelo2)$p.valeu

I tried do using the:

(for i in)

But I did not had success. How could I do it automatically using R??

Tnks!

Answer 1

Is a bit hard to tell from the question what you want, but if I was able to decipher something I think you want to create 2X2 matrix combinations from the columns of a 2X400 matrix.

So you would have 79800 combinations? I think.

choose(400,2) = 79800

I guess for the fisher.test i,j is the same as j,i and that i=j doesn’t make much sense, so

I would start by doing a function:

alelos = function(i,j){
alleys= matrix(c(df[,i],df[,j]),nrow=2,byrow=F)
#df is the 2X400 matrix, called data in the question
return(fisher.test(alleys)$p.value)
}

Then try the loops with for (i in 1:400) and a while perhaps? or something that makes a triangular matrix with the results. Such as:

I will give you an example with a vector of 10 columns.

same thing should work for 400.

set.seed(4)
df= matrix(c(sample(1:100,10,replace=T),sample(1:100,10,replace=T)),nrow=2)


resultmatrix = matrix(0,10,10)
#or 10x9 if you prefer

for(i in 10:1){
  j=1
while(i > j){
  resultmatrix[i,j]= alelos(i,j)

j=j+1
}
 }