On 2020-04-10 19:05 -0500, Ana Marija wrote:
> I am not sure what I am suppose to run
> from your codes. Can you just send me
> lines of codes which I should run?
> (without part where you are loading
> your data frames) (assuming my files
> are as I showed them)
Dear Ana,
try these lines:
plink.genome <-
read.table("plink.genome", header=TRUE)
SNPRelate::snpgdsBED2GDS(
"output4.bed",
"output4.fam",
"output4.bim",
"HapMap.gds")
genofile <-
SNPRelate::snpgdsOpen("HapMap.gds")
ibd <- SNPRelate::snpgdsIBDMoM(
genofile,
remove.monosnp=FALSE,
kinship=TRUE)
x <- paste(plink.genome$IID1,
plink.genome$IID2)
table <- paste(ibd$ID1, ibd$ID2)
idx <- match(x=x, table=table)
plink.genome[idx,]
Best,
Rasmus
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