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Question: GWAS with family data
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gravatar for Naomi Altman
3.7 years ago by
Naomi Altman6.0k
Naomi Altman6.0k 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
ADD COMMENTlink modified 3.7 years ago by Paul Geeleher1.3k • written 3.7 years ago by Naomi Altman6.0k
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gravatar for Stephanie M. Gogarten
3.7 years ago by
University of Washington
Stephanie M. Gogarten530 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 3.7 years ago by Stephanie M. Gogarten530
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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 3.7 years ago by Naomi Altman6.0k
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]]
ADD REPLYlink written 3.7 years ago by Juliet Hannah360
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gravatar for Paul Geeleher
3.7 years ago by
Paul Geeleher1.3k
Paul Geeleher1.3k wrote:
GenABEL will allow you to do this fairly easily. Notably, it is also very well documented. EMMAX may provide something a little more cutting edge when analysing family GWAS (but not in an R environment): http://www.nature.com/ng/journal/v42/n4/abs/ng.548.html Paul. On Tue, Apr 15, 2014 at 12:09 PM, Naomi Altman <naomi at="" stat.psu.edu=""> 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr. Paul Geeleher, PhD Section of Hematology-Oncology Department of Medicine The University of Chicago 900 E. 57th St., KCBD, Room 7144 Chicago, IL 60637 -- www.bioinformaticstutorials.com
ADD COMMENTlink written 3.7 years ago by Paul Geeleher1.3k
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