[Bioc-sig-seq] Shuffling genomic positions at random

[Ivan Gregoretti]

Dear Bioconductor connoisseurs,

Is there an algorithm to produce a random set of genomic positions?


In more detail now:

I have two sets of ChIP-seq peak locations. Say they are 10000 peaks
each. There is partial overlap between both sets. The question that I
need to answer is whether or not that overlap is statistically
significant.

I can answer that question if I can randomly shuffle one of the sets
many times and compute the overlap with the non-shuffled set.

IMPORTANT: some portions of the mouse genome must be excluded because
their are repetitive or poorly sequenced. For instance, those familiar
with the mm9 assembly know that the first 3 million bases of almost
all chromosomes are to be excluded.

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