Question: How to remove the high correlated SNPs in R
gravatar for zwang10
24 months ago by
United States
zwang100 wrote:

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.

ld snp • 896 views
ADD COMMENTlink modified 24 months ago by swti66900 • written 24 months ago by zwang100
gravatar for mbyvcm
24 months ago by
Cardiff, UK
mbyvcm350 wrote:

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.  

ADD COMMENTlink written 24 months ago by mbyvcm350

Can you tell me use which tool can convert matrix into PLINK files?

ADD REPLYlink written 24 months ago by zwang100

You have a few options. With a little manipulation in R you could easily generate a map and ped (file specs are here). Another option would be to use the R package snpStats to; i) convert your matric to a snpStats object, ii) write out PLINK files in R.

ADD REPLYlink written 23 months ago by mbyvcm350
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