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Re: st: haplologit-genetic association


From   Jane Maguire <Jane.Maguire@newcastle.edu.au>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: haplologit-genetic association
Date   Thu, 27 Aug 2009 09:40:29 +1000

Dear Neil

Thanks for the advice. Here is the output for other readers. "Rubbish" refers to the OR for variable cox2use and 
c._hap11*c.cox2use...


. xi: haplologit stroke i.cox2use i.aspirin i.nsaid i.gender i.agegroup2 i.bmigroup2 i.Diabetes4 i.HT
>  i.AF2 ///
>  (i.Smoker) if ~(inlist(kozak,.) & inlist(thrmet,.)), snpvars(kozak thrmet)  ///
>                    riskhap1("11", inter(cox2use))  ///
>                                         inher(d) happrefix(_hap) or 
i.cox2use         _Icox2use_0-1       (naturally coded; _Icox2use_0 omitted)
i.aspirin         _Iaspirin_0-1       (naturally coded; _Iaspirin_0 omitted)
i.nsaid           _Insaid_0-1         (naturally coded; _Insaid_0 omitted)
i.gender          _Igender_1-2        (_Igender_1 for gender==F omitted)
i.agegroup2       _Iagegroup2_1-2     (naturally coded; _Iagegroup2_1 omitted)
i.bmigroup2       _Ibmigroup2_1-2     (naturally coded; _Ibmigroup2_1 omitted)
i.Diabetes4       _IDiabetes4_0-1     (naturally coded; _IDiabetes4_0 omitted)
i.HT              _IHT_0-1            (naturally coded; _IHT_0 omitted)
i.AF2             _IAF2_0-1           (naturally coded; _IAF2_0 omitted)
i.Smoker          _ISmoker_1-3        (naturally coded; _ISmoker_3 omitted)

Building consistent haplotype pairs:

Obtaining initial haplotype frequency estimates from the control sample:

Haplotype frequency EM estimation

Number of iterations  =         18
Sample log-likelihood = -479.73979

  +------------------------+
  | haplotype | frequency* |
  |-----------+------------|
  |        00 |    .003216 |
  |        01 |     .11588 |
  |        10 |    .062492 |
  |        11 |    .818411 |
  +------------------------+
  * frequencies > .0020263

Performing gradient-based optimization:

Iteration 0:   Retrosp. profile log likelihood = -1643.8538  
Iteration 1:   Retrosp. profile log likelihood = -1453.0153  
Iteration 2:   Retrosp. profile log likelihood = -1451.7071  
Iteration 3:   Retrosp. profile log likelihood = -1451.6272  
Iteration 4:   Retrosp. profile log likelihood = -1451.6222  
Iteration 5:   Retrosp. profile log likelihood = -1451.6211  
Iteration 6:   Retrosp. profile log likelihood = -1451.6208  
Iteration 7:   Retrosp. profile log likelihood = -1451.6207  
Iteration 8:   Retrosp. profile log likelihood = -1451.6207  

Haplotype-effects logistic regression
Mode of inheritance: dominant                   Number of obs      =       987

Genetic distribution: Hardy-Weinberg equilib.   Number phased      =       973
Genotype: kozak thrmet                          Number unphased    =        14
                                                Number missing     =         0

                                                Wald chi2(13)      =    247.92
Retrosp. profile log likelihood = -1451.6207    Prob > chi2        =    0.0000

------------------------------------------------------------------------------
      stroke | Odds Ratio   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
 _Icox2use_1 |   3.05e-06   .0017547    -0.02   0.982            0           .
 _Iaspirin_1 |   1.787856   .3324477     3.12   0.002     1.241806    2.574018
   _Insaid_1 |   1.017781    .253331     0.07   0.944     .6248646    1.657765
  _Igender_2 |   1.446311   .2393843     2.23   0.026     1.045626     2.00054
_Iagegroup~2 |   9.470277   1.765575    12.06   0.000     6.571589    13.64756
_Ibmigroup~2 |   .5589643   .0981841    -3.31   0.001     .3961572    .7886797
_IDiabetes~1 |   1.853561   .3687461     3.10   0.002     1.255074    2.737438
      _IHT_1 |    2.43637   .4227256     5.13   0.000     1.734021    3.423198
     _IAF2_1 |    2.12824   .4636764     3.47   0.001     1.388579    3.261899
  _ISmoker_1 |   6.209872   1.606923     7.06   0.000     3.739538     10.3121
  _ISmoker_2 |   1.074069   .1920307     0.40   0.689      .756567    1.524814
      _hap11 |    1.03895   .3069367     0.13   0.897     .5822703    1.853809
             |
   c._hap11* |
   c.cox2use |   170300.5   9.80e+07     0.02   0.983            0           .
------------------------------------------------------------------------------

Haplotype frequencies

------------------------------------------------------------------------------
             |      Coef.   Std. Err.      z    P>|z|     [95% Conf. Interval]
-------------+----------------------------------------------------------------
      _hap00 |   .0016101   .0014436     1.12   0.265    -.0012194    .0044395
      _hap01 |   .1129663    .007536    14.99   0.000     .0981959    .1277366
      _hap10 |   .0650989   .0057849    11.25   0.000     .0537607    .0764371
      _hap11 |   .8203248   .0094228    87.06   0.000     .8018565     .838793
------------------------------------------------------------------------------


















>>> Neil Shephard <nshephard@gmail.com> 26/08/2009 5:47 pm >>>
On Wed, Aug 26, 2009 at 5:39 AM, Jane
Maguire<Jane.Maguire@newcastle.edu.au> wrote:
> Dear all
> Data is case control, snps are coded 0,1,2
> One gene, two snps. Haplotype for hap00 is quite rare and when interaction term (cox2use) is added the output is rubbish.

What does "rubbish" mean?

> I am not a biostatistician- am a Phd student in medicine and Public Health.

You'd benefit from getting your head round the basics of statistics in
the long run.  A good book is Intuitive Biostatistics by Harvey
Motulsky.  Not too heavy on the maths, but explains things very well.

> However, I think the problem is the numbers are too small...unless I have made a coding error? any advice?
>
> This command works- without interaction,
>
> xi: haplologit stroke i.cox2use i.aspirin i.nsaid i.gender i.agegroup2 i.bmigroup2 i.Diabetes4 i.HT i.AF2 ///
>  (i.Smoker) if ~(inlist(kozak,.) & inlist(thrmet,.)), snpvars(kozak thrmet) inher(d) ///
>                   riskhap1("11") ///
>                                         happrefix(_hap) or noemtable noemshow
>
> But this one doesn't,
>
> set more off
> xi: haplologit stroke i.cox2use i.aspirin i.nsaid i.gender i.agegroup2 i.bmigroup2 i.Diabetes4 i.HT i.AF2 ///
>  (i.Smoker) if ~(inlist(kozak,.) & inlist(thrmet,.)), snpvars(kozak thrmet)  ///
>                   riskhap1("11", inter(cox2use))  ///
>                                        inher(d) happrefix(_hap) or

As per above, what does "rubbish" mean?  If you could show the output
of running these two commands it would be more informative for those
on the list who might then be able to comment on what the problem is.

Neil


-- 
"The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data." ~ John Tukey (1986), "Sunset salvo". The American
Statistician 40(1).

Email - nshephard@gmail.com 
Website - http://slack.ser.man.ac.uk/ 
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