Hi, I'm using GENESIS to obtain a KING matrix and then use it for an association analysis on a common beandataset (220 samples 4,355 SNPs on 12 chromosomes)

I've successfully:

• imported the vcf (or ped) file
• converted it in gds
• run the snpgdsIBDKING (I have no family information so "all individuals are treated as singletons")

but:

• after running the kingToMatrix function I've got the following result: No clusters identified 220 samples with no relatives included (that it is strange) and the matrix is as follow:

  king.mat.r[1:5,1:5] 5 x 5 sparse Matrix of class "dsTMatrix"

ECa_r1 ECa004 ECa005 ECa006 ECa008 ECa_r1 0.5 . . . .
ECa004 . 0.5 . . .
ECa005 . . 0.5 . .
ECa006 . . . 0.5 .
ECa008 . . . . 0.5

I've also tried using a tomato dataset (131 sample 2700 SNPs) but I'm obtaining the same results.

Any help on this would be appreciated, Thanks

The kingToMatrix function is only needed if you are running the command-line version of KING outside of R and importing text files. If you are using sngdsIBDKING, getting a kinship matrix is much simpler:

king <- snpgdsIBDKING(gds)
kingMat <- king$kinship
dimnames(kingMat) <- list(king$sample.id, king$sample.id)

Thank you very much Stephanie, I didn't realize the matrix was included in the snpgdsIBDKING output.

Monica