How to remove the high correlated SNPs in R
Hello all!
I have a data set (matrix) of a gene, each row represents an individual, and each column represents a genotype score (0, 1, 2). How can I remove the high correlated (r=0.8) SNPs?
I was trying using SNPRelate. But it needs GDS file. But there is no column name of the matrix.
1 answer
Not an R solution, but you could try the pruning you data based on LD in PLINK; PLINK LD Prune. You would need to convert you matrix into PLINK files.
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