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MrOlm / inStrain

Bioinformatics program inStrain
MIT License
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Issue in statistical analysis of nucleotide diversity. #162

Open ChenTianYi99 opened 11 months ago

ChenTianYi99 commented 11 months ago

Hi, I know that nucleotide diversity will be blank if no positions have a base over the minimum coverage. So i wonder if the NA value should be 0 or be dismissed (for example in R, na.rm=TRUE should be set) in downstream statistical analyses.

Looking forward to your reply. Thank you in advance. Sincerely

MrOlm commented 11 months ago

Hi @ChenTianYi99 - the answer here depends on the exact statistical task you're performing, but in general I remove these values rather then set them to 0.

Best, Matt

ChenTianYi99 commented 11 months ago

Hi, Matt. Thank you very much for your response. I will try to remove the NA values in my statistical analyses.

Best Tianyi Chen