Ordered Polytomous Regression

[Mark]

Hi

Does GLU have the capability to do ordered polytomous regression,
applying constraints to the outcome of interest?

Thanks
Mark

[Jacobs, Kevin (NIH/NCI) [C]]

Hi Mark,

Currently the answer is no. We have a version in the works that can offload models to R that will be able to do that.

-Kevin

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[Mark]

Thanks Kevin

On a related note, then, I would like to transform my genotype data
from, say, AA, AG, GG, to 0,1,2, for use in other programs.

It looks like the commands --outformat=NAME or --outgenorepr=REP might
be the right commands, but I cannot find an example of their use.

I have a very large genotype file, so I was hoping GLU could do it
without me having to say what the coding should be for each SNP. If
this is the case, is there an output file that GLU provides, showing
me the coding GLU has chosen for each pair of alleles?

Mark



On May 17, 1:56 pm, "Jacobs, Kevin (NIH/NCI) [C]"

[Kevin Jacobs <jacobs@bioinformed.com>]

Hi Mark,

GLU can indeed export to a few formats that use 0/1/2 encoding.  The best two are PLINK and one called 'fud':

  glu transform mydata.lbat -o mydata.ped

or

  glu transform mydata.lbat -o mydata.fud

(your input can be in one of many possible formats based on extension)

-Kevin

[Kevin Jacobs <jacobs@bioinformed.com>]

Oh and both PLINK and FUD format include the ordered allele assignments, so no guessing is required.

-Kevin

[Mark]

Hi Kevin

Thanks for the quick responses.

The .ped files seems to retain the alphabetical coding.

The .fud file looks good, except it is in an `ldat' format, which
inevitably means some data gets cut off when importing into e.g.
STATA. Is there a .fud `sdat' equivalent, or can you think of another
way around?

Thanks
Mark



On May 21, 1:21 pm, "Kevin Jacobs <jac...@bioinformed.com>"

<bioinfor...@gmail.com> wrote:
> Oh and both PLINK and FUD format include the ordered allele assignments, so
> no guessing is required.
>
> -Kevin
>
> On Mon, May 21, 2012 at 8:20 AM, Kevin Jacobs <jac...@bioinformed.com> <
>
>
>
>
>
>
>
> bioinfor...@gmail.com> wrote:
> > Hi Mark,
>
> > GLU can indeed export to a few formats that use 0/1/2 encoding.  The best
> > two are PLINK and one called 'fud':
>
> >   glu transform mydata.lbat -o mydata.ped
>
> > or
>
> >   glu transform mydata.lbat -o mydata.fud
>
> > (your input can be in one of many possible formats based on extension)
>
> > -Kevin
>

[Nicholas Orr]

Hi Mark,

I think you can recode the ped file in PLINK using the --recode12 option

Nick

Nick Orr, PhD | Staff Scientist | Breakthrough Breast Cancer Research Centre | Division of Breast Cancer Research | Institute of Cancer Research | 237 Fulham Road | London | SW3 6JB | United Kingdom | nichol...@icr.ac.uk | +44 20 7153 5330 |

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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