Question: How to remove the high correlated SNPs in R
0
gravatar for zwang10
21 months ago by
zwang100
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 • 818 views
ADD COMMENTlink modified 21 months ago by swti66900 • written 21 months ago by zwang100
0
gravatar for mbyvcm
21 months ago by
mbyvcm330
Cardiff, UK
mbyvcm330 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 21 months ago by mbyvcm330

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

ADD REPLYlink written 21 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 21 months ago by mbyvcm330
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 572 users visited in the last hour