[GenABEL-dev] Inputting fully justified table into GenABEL

[L.C. Karssen]

Dear Nathan,

Thanks for your interest in the GenABEL project. Please see my comments
below.

On 21/06/12 05:20, Nathan Corbett wrote:
> Hello friendly developers!
> 
> I see that you have guides on how to input standard outputs into
> GenABEL, but not the entirely generic justified table (minimum number
> of columns to describe every data point).  Is anyone working on this?

As far as I know no one is working on this yet.

> It would be nice to have a common minimally structured format to
> start from.

Do you have a suggestion for this minimal format?

> 
> My specific case is one where I don't have bead studio, or the raw
> files, only the formatted outputs given to me by the contracted lab.
> Accordingly, since my files are not in one of the listed formats, I
> am looking at a tricky situation.

Would it make sense to format your output files to MaCH or Impute format
and then use the regular import functions?
Is your data in binary format or plain text?

I'm a bit hesitant to add a new import format, because it seems to me
that people with non-matching import formats will always have to do some
shuffling of columns. Wouldn't a bit of GAWK scripting solve most import
problems?


Best regards,

Lennart.

> 
> Best regards,
> 
> Nathan Corbett UBC Experimental Medicine, Vancouver, Canada 
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> list genabel-devel at lists.r-forge.r-project.org 
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>
> 
-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

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