[BioC] linkage analysis

[Sean Davis]

On Monday 18 December 2006 12:27, Theresa Scharl wrote:
> Hi,
>
> I have Affymetrix 10k SNP data for 17 members of a family with a special
> disease (8 affected - 9 unaffected) and want to perform some kind of
> linkage or association analysis. The problem is that data is only
> available for about half the members of this family. There is only one
> person where the data of both father and mother is available.
>
> Any suggestions on how to analyze this kind of data would be very much
> appreciated!

It has been a while since I worked in that field, but you have looked at 
genehunter and merlin?  As for missing data, that is the norm for 
family-based studies; most software for linkage analysis use likelihood-based 
methods that can account for the missing data.

Sean