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

[L.C. Karssen]

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). 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).

I agree completely with Maarten that opening a filevector file for each
SNP will be an I/O killer.


Lennart.

> 
> best,
> Maksim
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> genabel-devel at lists.r-forge.r-project.org
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L.C. Karssen
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lennart at karssen.org
http://blog.karssen.org

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