question about "low variance"

suchestoncampbelllab / gwasurvivr

GWAS Survival Package in R

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question about "low variance" #22

Open DrGojiMori opened 3 years ago

DrGojiMori commented 3 years ago

Hi!

The description says ".snps_removed extension containing SNPs that were removed due to low variance or user-defined thresholds." What is the definition of "low variance"? It seems that some SNPs are removed even though they meet the conditions I defined, and I think "low variance" is the reason.

Thank you for help!

aarizvi commented 1 year ago

Low variance typically means that the standard deviation of that SNP is sd < 1e-04. We removed those SNPs because the model would not converge with them present.