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HenrikBengtsson / illuminaio

🔬 R package: This is the Bioconductor devel version of the illuminaio package.
http://bioconductor.org/packages/devel/bioc/html/illuminaio.html
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idat to vcf conversion #12

Open zillurbmb51 opened 4 years ago

zillurbmb51 commented 4 years ago

Hello, I have SNP array data for 668 cancer cell lines (illumina 2.5M). I can read them using readidat function of illuminao and can retrieve following information. I want to convert those idat files into vcf/plink format. Is there any way to do this? Best, Zillur `> head(idat1$nFields) [1] 19

head(idat1$fields) fieldCode byteOffset Bytes nSNPsRead 1000 206 0 IlluminaID 102 210 0 SD 103 10495902 0 Mean 104 15743748 0 NBeads 107 20991594 0 MidBlock 200 23615517 0 head(idat1$nSNPsRead) [1] 2623923 head(idat1$Quants) Mean SD NBeads 10600301 7079 1190 8 10600305 199 138 5 10600309 12633 1750 11 10600313 2639 462 11 10600316 6404 776 6 10600322 13636 988 6 dim(idat1$Quants) [1] 2623923 3 head(idat1$MidBlock) [1] 110600301 110600305 110600309 110600313 110600316 110600321 head(idat1$RedGreen) [1] 0 head(idat1$Barcode) [1] "6317404081" idat1$Barcode [1] "6317404081" head(idat1$ChipType) [1] "BeadChip 4x10" head(idat1$RunInfo) RunTime BlockType BlockPars
[1,] "10/13/2011 5:27:17 PM" "Decoding" "CallsToUsed=2836129|CallsToUnused=553|CallsToInvalid=102950"
[2,] "11/7/2011 9:53:56 AM" "Scan" "sherlockID=N133|ScannerID=N133|Username=SciOps|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.3.28" [3,] "11/7/2011 9:53:56 AM" "Register" "Algorithm=StandardGeneric"
[4,] "11/7/2011 9:53:56 AM" "Extract" "Algorithm=StandardWithBackground"
[5,] "10/13/2011 5:29:09 PM" "Decoding" "CallsToUsed=2792803|CallsToUnused=563|CallsToInvalid=78722"
[6,] "11/7/2011 9:55:03 AM" "Scan" "sherlockID=N133|ScannerID=N133|Username=SciOps|FPGAVersion=4.0.20|SoftwareAppication=iScan Control Software|SoftwareVersion=3.3.28" BlockCode CodeVersion [1,] "AutoDecode" "2.5.6"
[2,] "iScan Control Software" "3.3.28"
[3,] "iScan Control Software" "3.3.28"
[4,] "iScan Control Software" "3.3.28"
[5,] "AutoDecode" "2.5.6"
[6,] "iScan Control Software" "3.3.28"
dim(idat1$RunInfo) [1] 20 5 head(idat1$Unknowns) $MostlyNull [1] ""

$MostlyA [1] "R04C01"

$Unknown.1 [1] ""

$Unknown.2 [1] "WG0118064-DNAD09_SAM636382"

$Unknown.3 [1] ""

$Unknown.4 [1] "WG0118064-DNA"

dim(idat1$Unknowns) NULL str(idat1$Unknowns) List of 7 $ MostlyNull: chr "" $ MostlyA : chr "R04C01" $ Unknown.1 : chr "" $ Unknown.2 : chr "WG0118064-DNAD09_SAM636382" $ Unknown.3 : chr "" $ Unknown.4 : chr "WG0118064-DNA" $ Unknown.5 : chr "D09"`