Transforming Plink Files
Does anyone have any suggestions for combining .ped & .map files from Plink and transforming them into a different format? For example, the peds look like this:
#FID IID PAT MAT SEX STATUS G1 G2 G3 G4 G5 G6 G7 G8 G9 G10
12322 12322A 0 0 1 1 1 1 1 1 1 1 1 1 2 1
12322 12322B 0 0 2 0 1 1 1 1 2 2 2 1 1 2
12322 12322C 0 0 2 1 2 1 1 1 1 1 1 1 1 1
and the maps look like this:
#CHR G GD BP
1 1_135195_A/G 0 135195
1 1_135203_G/A 0 135203
1 1_136596_GGGG/- 0 136596
1 1_136604_G/C 0 136604
1 1_136619_G/A 0 136619
1 1_136620_C/T 0 136620
1 1_136635_T/G 0 136635
1 1_136645_G/- 0 136645
1 1_136652_A/G 0 136652
1 1_136779_G/A 0 136779
And what I'd like is this:
1_135195_A/G 1_135203_G/A 1_136596_GGGG/- 1_136604_G/C 1_136619_G/A 1_136620_C/T 1_136635_T/G 1_136645_G/- 1_136652_A/G 1_136779_G/A STATUS
1 1 1 1 1 1 1 1 2 1 1
1 1 1 1 2 2 2 1 1 2 0
2 1 1 1 1 1 1 1 1 1 1
Where the 2nd column in the 2nd file becomes the header of the third file and the 6th column of the 1st file becomes the final column of the 3rd file.
3 answers
This works:
ped <- read.table ("/pathtodata.ped")
map <- read.table ("/pathtodata.map")
map$V1 <- map$V3 <- map$V4 <- NULL
tmap <- t(map)
ped$V1 <- ped$V2 <- ped$V3 <- ped$V4 <- ped$V5 <- NULL
status <- ped$V6
ped$V6 <- NULL
colnames(ped) <- c(tmap)
ped$Status <- status
Look into --recodeA option in plink. That would create single *.raw format. http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#recode
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