[R] need help to generate an intersection matrix

Li, Aiguo (NIH/NCI) [E] liai at mail.nih.gov
Thu Feb 2 20:54:43 CET 2017

Dear all,

I am new to r script and run into some difficulty with this simple task.
Here is my data: I need to find out the number of mutual intersected elements as shown below
pathway1             A             B             C              D             E
pathway2             A             C              F
pathway3             B             D             E

                                pathway1             pathway2             pathway3
pathway1             5                                              2                                              3
pathway2             2                                              3                                              0
pathway3             3                                              0                                              3

here is my script
tb = matrix(data =NA, nrow = 3, ncol = 3)
for(i in 1:3){
  for(j in 1:3){

  tb[i,j]=length(intersect(data[i,][!is.na(data[i,])], data[j,][!is.na(data[j,])]))


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