Question: How to get imputation accuracy/quality after using IMPUTE2?
1
gravatar for Wan Shi Tong
22 months ago by
Wan Shi Tong60
Wan Shi Tong60 wrote:

I know I might be missing something obvious, but how do I get the accuracy/quality of my imputation after using IMPUTE2 (or any imputation tool)? How is the quality of an imputation measured?

Thank you!

statistics impute impute2 • 1.1k views
ADD COMMENTlink modified 22 months ago • written 22 months ago by Wan Shi Tong60
3
gravatar for Wan Shi Tong
22 months ago by
Wan Shi Tong60
Wan Shi Tong60 wrote:

I actually figured it out. Incase anyone ever has the same question. IMPUTE2 outputs a file called info where it has imputation quality information. Depending on the command line arguments you choose you can get more specific statistics. https://mathgen.stats.ox.ac.uk/impute/output_file_options.html#info_metric_details

ADD COMMENTlink written 22 months ago by Wan Shi Tong60
1

If at all possible, I think you should also try analysis strategies that don't require imputation, but I appreciate your feedback (I was not familiar with that link).

ADD REPLYlink modified 22 months ago • written 22 months ago by Charles Warden8.0k
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