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

You might benefit from formally modelling the semantics of your data. If you have ranges on the genome, use the GenomicRanges package from Bioconductor.

library(GenomicRanges)
gr <- makeGRangesFromDataFrame(df, keep.extra.columns=TRUE)

This is a GRanges object, which formally understands the notion of genomic location, so these operations just work:

hits <- findMatches(gr, gr)
tab <- table(motif1=gr$motif[queryHits(hits)],
             motif2=gr$motif[subjectHits(hits)])
subset(as.data.frame(tab, responseName="count"), motif1 != motif2)