[BioC] ways to measure runs of homozygosity?

[Matthew Keller]

Hi all,

I am about to get back into a project re runs of homozygosity. This
summer I used the Affy CNV algorithm, which used HMMC to determine
whether a given SNP was within a homozygous run. I have since seen the
Double Helix has an algorithm as well - although it seems simpler than
the Affy one (which in itself is not a bad thing, but I don't think
that the Double Helix algorithm is 'forgiving' of heterozgote calls
that exist in a long stretch of homozygotes and that are therefore
probably errors). But I'd much rather use R than a proprietary
software package.

So is anyone here aware of a way to judge runs of homozygosity in 100
or 500K SNP data using R or Bioconductor? If so, what type of
algorithm is used? Thanks in advance,

Matt



-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com