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Old 02-02-2016, 05:08 PM   #1
Location: usa

Join Date: Jan 2016
Posts: 13
Default How to remove the high correlated SNPs in R software

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.

Since I am using Monte Carlo to calculate the p-value of my method (comparing power of association test), I need to remove the high correlated SNPs for each replicate.

Last edited by Mike_Brown; 02-02-2016 at 05:57 PM.
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