export.merlin() - pheno-information ?

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

export.merlin() - pheno-information ?

Postby MariaG » Tue Mar 01, 2011 10:25 am

Hi :)

(1) In export.merlin() there is an option "traits", which supposes to input the number of phenotypes for extraction.
Isn't is more straightforward to input names instead of numbers and so to keep the information about the pheno-names?
The thing is, that at the moment in the merlin-output files the information about the extracted phenotypes is totally lost:

in .ped there is no colnames
in .dat the traits have all the same name: "faket"+number.

(2) And the other thing. If I plan to use export.merlin format as an input for MACH (to impute data) and then I plan to use the results in ProbABEL, I would need an extra file: .pheno. For sure, I can prepare .pheno file manually or use export.plink() (which is time consuming), but why not to incorporate this option into the export.merlin() ?

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

Re: export.merlin() - pheno-information ?

Postby yurii » Wed Mar 09, 2011 11:31 pm

in .ped there is no colnames


This we can do nothing about (and should not): otherwise MERLIN could not process it!

in .dat the traits have all the same name: "faket"+number.


This is something we can improve, thanks for suggestions. Should file in a feature request. Can you try to do so at

https://r-forge.r-project.org/tracker/?group_id=505

if willing, please communicate to me in private (through e-mail) in case of any difficulties.

(2) And the other thing. If I plan to use export.merlin format as an input for MACH (to impute data) and then I plan to use the results in ProbABEL, I would need an extra file: .pheno. For sure, I can prepare .pheno file manually or use export.plink() (which is time consuming), but why not to incorporate this option into the export.merlin() ?


This is something we can potentially implement, but I actually would not go for a trouble of doing so. Imputations take so much effort, that by the time you are done you will almost for sure forget you exported a PHE at the start :) Also, making a PHE-file is so easy.
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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