[GenABEL-dev] function for conversion a plink format file to a GenABEL format file

[L.C. Karssen]

How difficult would it be to import .bed files [1] instead of the text
conversion? Given the binary data of both the .bed and the GenABEL
format, wouldn't conversion be much quicker?


Lennart.

[1] http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml


On 11/22/2013 09:54 AM, Yurii Aulchenko wrote:
> Too slow, too difficult for the user, or both? :)
> 
> On Friday, November 22, 2013, Maksim Struchalin wrote:
> 
>     Yes. Looks like it was a bad idea to use plink R-plugin for
>     converting plink files to *ABEL format.
>     Maksim
> 
>     On 18/11/2013 18:48, Yury Aulchenko wrote:
>>     I would say that in principle DatABEL::text2databel is the
>>     "natural" way to go from text-files to DatABEL-files
>>
>>     The problem is that 'regular' text input may be allele by allele,
>>     not genotype by genotype... (e.g. data are in format "A G", or
>>     "A/G", not "0" or "1" or "2"). 
>>
>>     Y
>>
>>     On Nov 15, 2013, at 17:48 PM, L.C. Karssen <lennart at karssen.org>
>>     wrote:
>>
>>>     Hi Maksim,
>>>
>>>     On 15-11-13 05:53, Maksim Struchalin wrote:
>>>>     An easy way to write a function for conversion a plink format
>>>>     file to a
>>>>     GenABEL format file:
>>>>
>>>>     Use plink support of 'plug-in' functions
>>>
>>>     Nice find. I didn't know that existed.
>>>
>>>>     (http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml
>>>>     <http://pngu.mgh.harvard.edu/%7Epurcell/plink/rfunc.shtml>).
>>>>     This allows us
>>>>     to write a simple R script (myscript.R) which is called by plink
>>>>     (plink
>>>>     --file mydata --R myscript.R). plink reads the file mydata
>>>>     (which is in
>>>>     plink format) and iteratively, SNP by SNP, trasfer all the data to a
>>>>     script myscript.R. This script contains a function
>>>>     Rplink(PHENO,GENO,CLUSTER,COVAR) which will take every SNP (GENO
>>>>     variable) and store it in a *flv format through calling DatABEL
>>>>     functions.
>>>>
>>>>     The whole process of conversion will look like this:
>>>>
>>>>     1) User asks GenA convert plink file to GenA file
>>>>     2) GenA looks weather the plink is installed. If it is not
>>>>     installed,
>>>>     then GenA goes to a plink site and download/install it itself
>>>>     (use an R
>>>>     function "download.file" from "utils" package)
>>>>     3) GenA run a simple line: system('plink --file mydata --R
>>>>     myscript.R')
>>>>     4) Rplink function (from myscript.R) gets every SNP and stote it
>>>>     in *flv
>>>>     format. This function creates an flv file and then open and
>>>>     close it for
>>>>     saving every single SNP.
>>>>     5) Work is Done
>>>
>>>     I'm not sure how portable it is to download and run plink. Also, the
>>>     plink page says: Currently, there is only support for R-plugins for
>>>     Linux-based and Mac OS PLINK distributions.
>>>
>>>>
>>>>     The only issue is how fast the converssion will run: how much
>>>>     time does
>>>>     it take to open a filvector file, store one SNP and close it? I
>>>>     can not
>>>>     find a DatABEL R function for adding SNP to a flv file. Is there a C
>>>>     DatABEL function which can do it?
>>>
>>>     Wouldn't it be easier/possible to use plink to export to text
>>>     (.csv) and
>>>     then use filevector's txt2fvf binary (of course this could be
>>>     done from
>>>     R using system())?
>>>
>>>     I'm also wondering if going per SNP is really necessary. If I
>>>     understand
>>>     it correctly the R script (myscript.R) has to have a function called:
>>>     Rplink <- function(PHENO,GENO,CLUSTER,COVAR)
>>>     where GENO is the matrix of genotypes. So we could write that into a
>>>     DatABEL file at once. Of course you may want to do this per
>>>     chromosome
>>>     to reduce memory consumption (not sure how plink/R would handle large
>>>     data sets).
>>>
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
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> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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