[SOLVED] Convert from GenABEL into PLINK format

Questions about GenABEL (aka *ABEL) suite of packages
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MariaG
GenABEL specialist
GenABEL specialist
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Joined: Thu Feb 03, 2011 12:29 pm

[SOLVED] Convert from GenABEL into PLINK format

Postby MariaG » Mon Feb 07, 2011 10:12 am

Hi :)

Is there easy possibility to convert back to PLINK format from the GenABEL?
I'm trying to compose plink.ped file manually, based on GenABEL dataset. However I can't find how to reconstract a family-structure (family,id,mo,fa)?
For example, with gwaa.data@phdata$id I can get only individual ids ...

Thanks

Maria
Last edited by MariaG on Mon Feb 28, 2011 3:15 pm, edited 1 time in total.

yurii
GenABEL developer
GenABEL developer
Posts: 263
Joined: Fri Jan 21, 2011 5:20 pm

Re: Convert from GenABEL into PLINK format

Postby yurii » Mon Feb 07, 2011 5:08 pm

did you try 'export.plink'?

Note this is relatively new function available from 1.6-3 on, with a bug fixed in 1.6-5. So you need to use the latest version of GA.
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii

MariaG
GenABEL specialist
GenABEL specialist
Posts: 36
Joined: Thu Feb 03, 2011 12:29 pm

Re: Convert from GenABEL into PLINK format

Postby MariaG » Tue Feb 08, 2011 11:12 am

Unfortunatelly, "export.plink" doesn't work - I always get an error message, which asks to close the R session. I would suppose, it's still a "memory problem".
In somedays I plan to install Linux-64, will see if the function will wok there..

MariaG
GenABEL specialist
GenABEL specialist
Posts: 36
Joined: Thu Feb 03, 2011 12:29 pm

Re: Convert from GenABEL into PLINK format

Postby MariaG » Tue Feb 08, 2011 11:14 am

And anyway, I just wonder, if Family-info is saved somewhere among GenABEL's variables?

yurii
GenABEL developer
GenABEL developer
Posts: 263
Joined: Fri Jan 21, 2011 5:20 pm

Re: Convert from GenABEL into PLINK format

Postby yurii » Tue Feb 08, 2011 2:06 pm

re: export.plink(). There was a bug in this procedure, now fixed. Please try GenABEL v 1.6-5 (now available from CRAN) and let us know the results!
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii

yurii
GenABEL developer
GenABEL developer
Posts: 263
Joined: Fri Jan 21, 2011 5:20 pm

Re: Convert from GenABEL into PLINK format

Postby yurii » Tue Feb 08, 2011 2:10 pm

I just wonder, if Family-info is saved somewhere among GenABEL's variables?


No, GenABEL does not assume that you know family, and does not require that. Basically, there is no need -- we estimate relationship from the genome!

You can of cause keep family structure as part of phenotypic data if needed.

export.plink() constructs 'empty' pedigree, sintactically corerct, but all parents are "0" -- so, 'independent'
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii


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