[Bioc-sig-seq] Pairwise comparisons of peak sets (for ChIP-seqs or anything else)

[Ivan Gregoretti]

Hello everyone,

How do I draw a pairwise comparison table?

Simplified example of the problem:

1) lets say I have several sets of ChIP-seq peaks from several
experiments: setA, setB, setC, etc. Many sets.

2) I know how many peaks in common are held by each pair of sets. For
instance, setA and setB have 300 peaks in common (overlaps). I can
create a square matrix to hold all pairwise values.

3) Now I want to draw something like a square table where both columns
and rows are labelled setA, setB, setC, etc. In position [setA, setB]
I would write 300 (and so I would on position [setB, setA]).

Is there any R function created to address this need? Perhaps
something like a general purpose heat map?

Any pointer would be appreciated.

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878