The kinship2 package implements a mixed model for family data. It is not GWAS specific, but has been used in GWAS studies with family data. On Wed, Apr 16, 2014 at 3:00 PM, NAOMI S ALTMAN <naomi@stat.psu.edu> wrote: > Thanks, Stephanie. > > This was actually to demonstrate GWAS to my course. The only GWAS > analysis I had done previously had no family info - most of the folks I > talk with have nuclear families. So even if the association is bogus, I am > glad you did it this way - it brought up a number of issues I was not aware > of at that time, which means that my class is now aware of the issues. > > Did you notice that there was a pretty strong association between race and > your status variable? > > --Naomi > > > > On 4/16/2014 11:23 AM, Stephanie M. Gogarten wrote: > >> Hi Naomi, >> >> Just a word of caution on the GWASdata package - the case-control status >> for those samples is not real, I made it up for the GWASTools examples by >> randomly assigning case status to HapMap samples. >> >> I'm afraid I don't have any advice on family studies - when I've done >> analyses with GWASTools I've selected only unrelated samples for the >> association tests, which is presumably not what you want to do for a family >> study. >> >> Stephanie >> >> On 4/15/14 1:09 PM, Naomi Altman wrote: >> >>> Is there software in R for doing GWAS analysis with family case- control >>> data? >>> >>> I started with the data in GWASdata. This is a set of 13 families of 2 >>> ethnicities. So just treating the data as a bunch of 2x3 tables is >>> clearly not correct. >>> >>> I cannot seem to find any software that is extensible. The workflow in >>> GWAStools seems OK (I did not do all of it) but it is a pipeline - not >>> really the same as controlling my own analysis. >>> >>> Thanks >>> --Naomi >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]