Issue in statistical analysis of nucleotide diversity.

[ChenTianYi99]

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]

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]

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

Best
Tianyi Chen