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Missing data in ldNe #36

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@jdalapicolla

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@jdalapicolla

Hello Eric,

My name is Jeronymo and I'd like to estimate Ne using strataG similarly to NeEstimator. My dataset shows 6.3% of missing, represent one panmictic population, and when I used the function ldNe:

Ne = ldNe(snps_gtypes, maf.threshold = 0, by.strata = TRUE, ci = 0.95, drop.missing = TRUE, num.cores = 4)

Ne is estimated excluding missing values, same values than NeEstimator v2.1. When I used "drop.missing = TRUE", NULL is returned:

Warning message:
Can't compute ldNe in '1' because loci are missing genotypes and 'drop.missing = FALSE'. NULL returned.

I would like to know how I should proceed in your opinion:

  1. Am I doing something wrong? My script is here: https://github.com/jdalapicolla/Ne_StrataG.R/blob/master/Ne_Estimation.R
  2. Should I impute missing values by the mode or mean? If yes, what functions or packages do you recommend?
  3. Should I use NeEstimator when there are missing values in my dataset?
  4. Is there any way to implement the NeEstimator's solution for missing values in the function ldNe?

Thank you so much for your time,
Best regards,
Jeronymo Dalapicolla

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