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From genotype raw data .idat to PLINK files
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6.2 years ago
Armand • 20
Spain

Dear all,

I have several raw data (exome genotyping) : _Red.idat _Grn.idat

.. and also the illumina data mapping , a file with this columns :

"Family ID","Individual ID","Sample ID","Genotyping Chip Barcode","Genotyping Chip Type","Final Report Name","Sex","Study Role","Birth Year Month"

....

(where Genotyping Chip Barcode is something like "4252475888_A" and Genotyping Chip Type like "1M-Duov3")

I have different platforms, but now I am focused the data from 1M-Duov3)

I would like to generate the PLINK file. I am using the _crlmm_ R package in order to try to get, at least, the .ped plink genotype file. I am figuring out how to launch successfully _genotype.Illumina_ function.

I am following : http://master.bioconductor.org/packages/release/bioc/manuals/crlmm/man/crlmm.pdf

cnSet <- genotype.Illumina(sampleSheet=samplesheet_subset,
arrayNames=samplesheet_subset$Sample.ID,
path=datadir,
arrayInfoColNames=samplesheet[wh_array_name_pos,"Genotyping.Chip.Barcode"],
cdfName="human1mduov3b",
batch=rep("1", nrow(samplesheet_subset)))

 It seems that _cdfName_ according to 1M-Duov3 should be  "human1mduov3b".

  _samplesheet_subset_  a subset data.frame **  illumina data mapping** file with a subset of .idat files **.** (I am using 38           samples -parents, probands, sibiling, ..)

  _arrayNames_ I don 't know what it reefers to... (I try to pass the different sample ID  : samplesheet_subset$Sample.ID)

  _batch_ following the example ... (the number of rows of samplesheet_subset)

When I launch, I got this error :

"

Instantiate CNSet container.
Error en constructInf(sampleSheet = sampleSheet, arrayNames = arrayNames,  : 
  Missing some of the *Grn.idat files

"

But I think that all the .idat files are there ...(_R01C01_Grn.idat, _R01C02_Grn.idat, _R01C01_Red.idat,*_R01C02_Red.idat)

[... and I suppose that every .idat file contain variouse samples ..]

Thanks for your help,

Cheers,

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I encounter the same error.

Have you manage to solve that?

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13 months ago

Had the same issue, make sure your files have a .idat extension and are not gzip-compressed. And that the path directory begins with a / and is input as a string (with " "). Worked for me

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