[GenABEL-dev] function for conversion a plink format file to a GenABEL format file
L.C. Karssen
lennart at karssen.org
Fri Nov 22 11:08:16 CET 2013
Thanks Maarten, that's a good finding. It does seem to return the data
(incl. genotype data) in a list. I'm not sure how well that will work
RAM-wise for large data sets. On the other hand the function does allow
SNP selection, so maybe conversion could be done per chromosome.
Lennart.
On 11/22/2013 10:54 AM, Maarten Kooyman wrote:
> There is also a function in to read bed files in the bioconductor
> snpStats package. This might be a vantage point.
>
> see : search.bioconductor.jp/codes/6594
>
> Maarten Kooyman
>
> On 11/22/2013 10:04 AM, L.C. Karssen wrote:
>> 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
>>>
>>> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
>>> <http://twitter.com/YuriiAulchenko> ] [ Blog
>>> <http://yurii-aulchenko.blogspot.nl/> ]
>>>
>>>
>>>
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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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