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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:
- Am I doing something wrong? My script is here: https://github.com/jdalapicolla/Ne_StrataG.R/blob/master/Ne_Estimation.R
- Should I impute missing values by the mode or mean? If yes, what functions or packages do you recommend?
- Should I use NeEstimator when there are missing values in my dataset?
- 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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