Biostar Beta. Not for public use.
From genotype raw data .idat to PLINK files
0
Entering edit mode
20 months ago
Armand • 20
@Armand2407

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,

R sequencing genotype • 4.1k views
ADD COMMENTlink
0
Entering edit mode

I encounter the same error.

Have you manage to solve that?

ADD REPLYlink
0
Entering edit mode
20 months ago
@eva.gradovich55257

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

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.3