Hi James,
Just to clear up any further confusion, currently for -method newml on the X chromosome:
1. if you do not use -stratify_on sex then you are estimating a single effect size parameter, and this is under a model of complete X inactivation in females.
2. if you use -stratify_on sex (and -cov_names sex) then you are estimating effects separately in males and females (i.e. as though running males and females in separate SNPTEST runs). This allows for different effects in males and females, or incomplete inactivation in females. Effect sizes are all still relative to an X inactivation model, e.g beta_males = beta_females corresponds to an X inactivation model, while if there is no inactivation at all and each copy of the allele has the same effect, you would get beta_females ~ 2 x beta_males. (Here beta is the effect size on log-odds scale.)
3. I should probably add a -no_X_inactivation flag that turns off the X inactivation model - there’s no such option at the moment.
Hope this is clear(er)!
Best,
Gavin.
Dear Gavin,
Thanks for that I was confused.
It’s now running using –cov_names with –method newml and I have included sex as a covariate to allow for incomplete X inactivation.
I also updated my .gen files with X in the first column which seemed to help rather than using the –assume_chromosome option.
Many Thanks
James
From: Oxford Statistical Genetics Software [mailto:[log in to unmask]] On Behalf Of Gavin Band
Sent: 28 November 2013 17:09
To: [log in to unmask]
Subject: Re: [OXSTATGEN] Stratifying on multiple covaritaes for non PAR X chromosome using SNPtestv2.5
Hi James,
I'm not sure quite what you mean here. Generally you would use -cov_names (or one of the similar options) to include covariates in your scan.
Option -stratify_on is specifically designed to allow estimation of separate parameters in each level. To handle population structure, you probably just want to use -cov_names as for the autosomes here?
On 28 Nov 2013, at 16:52, James Uphill (Prion) wrote:
Is it possible to stratify on 4 covariates simultaneously for the X chromosome using SNPtestv2.5?
Reading the instructions it implies that I have to use –method newml and this can only handle a single covariate at a time i.e sex.
I have been using 4 covariates to allow for population stratification for autosomes using –method score option and would like to do a similar thing for the X chromosome.
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