How to deal with the "." in the vcf file?

stephenslab / susieR

R package for "sum of single effects" regression.

https://stephenslab.github.io/susieR

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How to deal with the "." in the vcf file? #230

Closed YuhaoDoong closed 3 months ago

YuhaoDoong commented 6 months ago

When "0|0", "0|1", and "1|1" are transformed into 0, 1, and 2, then how to deal with the "." in the vcf file?

as susie function can not allow NA in the input X

pcarbo commented 6 months ago

@YuhaoDoong You are correct that susie does not allow missing values (NAs). If you have a very small number of missing values (say, <1%), I think it would be safe to set the missing values to the column mean. Otherwise, you will have to look into imputing the genotypes. I'm not current on the latest methods for doing this, so you will have to do some research to determine the method that is most suitable for your experimental setup.