Transcription factor co-localization p-values

Question

[Vishal]

I have ChIPSeq peak data for TF A and TF B in bed format. On examining these in a genome browser together, I see that there are many instances when TFBS for both A and B are close to each other. What kind of statistical test can I do (and how) to check if the two TFs co-localize.

In other words, if I have a list of genomic loci from one experiment (it doesn't really matter how I got these) and want to test if these genomic loci are always near (say < 1kb) from another completely independent set of genomic loci. What is the best way to get this? I want to get some significance value as well.

Answer 1

[jared.andrews07]

regioneR seems to be what you want.