issue with running gl.report.ld.map

[Jessica Bruce]

Hi eveyrone,

I'm hoping someone can help me work out what I've got happening in my data:

I've got this as my suggested code from my supervisor (exceot the verbosity, I was hoping it would tell me more):

df.LDmap <- gl.report.ld.map(df.8, maf = 0.1,
                             ind.limit = 10,
                             ld_threshold_pops = 0.5,
                             verbose = 5)

which runs fine to begin with and then hits this snag (last line):

Starting gl.report.ld.map [dartR vers. 2.9.7 Build = Jody ] Processing genlight object with SNP data Skipping population Black Landing from analysis because it has less than 10 individuals. Calculating pairwise LD in population Block 892 Calculating pairwise LD in population Bondo Calculating pairwise LD in population Broken Cart Trail Error in 1:nLoc(x) : NA/NaN argument

I am guessing it's something odd in the way i've input my data in the first place, but I've been through 6 filter steps already without an issue and so my data should already be somewhat "clean"? Is there a way for me to query what is happening? Or should I be filtering on NA calls before this stage?

Thanks so much,

Jess

[Claudia Escobar]

Hi Jess,

I am having the same problem but only on Linux. It works well on Windows. Is it the same for you?

Kind regards,

Claudia