Question: PRSice: Imputation and clumping
0
gravatar for muraved
3 months ago by
muraved10
United States
muraved10 wrote:

I am trying to use PRSice. Unfortunately, my target sample has fewer SNPs than my discovery/base sample, as it comes from different platforms. My question is of a methodological nature: I could of course impute the missing SNPs, and PRSice explicitely mentions it can handle such information. However, PRSice also performs clumping. If I'm not mistaken, imputation fills in missing SNPs using linkage disequilibrium information, while clumping then tries to estimate LD and reduce the SNPs to an independent set. Wouldn't imputation and clumping pretty much cancel out then? I'm not sure what the best practice is in this situation.

ADD COMMENTlink modified 10 weeks ago by Sam2.2k • written 3 months ago by muraved10

PRSice has its google group for quick answers https://groups.google.com/forum/#!forum/prsice

ADD REPLYlink written 12 weeks ago by Rm7.8k
1
gravatar for Sam
10 weeks ago by
Sam2.2k
London
Sam2.2k wrote:

The thing is, we only perform clumping on SNPs that were found in both the target and base file. By using the imputed data, you increase the coverage and might result in more post-clumped SNPs, therefore increase amount of information and possibly increase the performance of your PRS model

ADD COMMENTlink written 10 weeks ago by Sam2.2k
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