Count every possible pair of values in a column grouped by multiple columns

Question

I have a dataframe that looks like this (this is just a subset, actually dataset has 2724098 rows)

> head(dat)

chr   start  end    enhancer motif 
chr10          


        

Answer 1

What about this?:

res1<- split(dat$motif,dat$id)
res2<- lapply(res1,function(x) combn(x,2))
res3<- apply(do.call(cbind,res2),2,function(x) paste(x[1],x[2],sep="_"))

table(res3)