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.
cnSet <- genotype.Illumina(sampleSheet=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,