Closed EmiCarr closed 5 years ago
NickJeff13
commented
5 years ago Hi, I have not seen that error before, is it possible to share your data or a subset of it and I can try to troubleshoot? If so you can email it to nick.jeffery@dfo-mpo.gc.ca
NickJeff13
commented
5 years ago There is an issue with the genepop_rubias function removing the first 2 loci for some reason, I'll push a fix to this which should help with running the rubias mixture analysis.
EmiCarr
commented
5 years ago Ok, thanks a lot! Let me know when you are done with the fix.
Have a nice day,
Emilie
Le jeu. 23 mai 2019 à 11:42, Nick Jeffery notifications@github.com a écrit :
There is an issue with the genepop_rubias function removing the first 2 loci for some reason, I'll push a fix to this which should help with running the rubias mixture analysis.
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NickJeff13
commented
5 years ago Ok I made the fix, try reinstalling genepopedit, run the genepop_rubias function, and see if it runs in rubias.
Hi,
I am using genepopedit to convert a genepop to a rubias file. However, when I try to perform a mixture analysis, I have this error :
Error in check_refmix(reference, gen_start_col, "reference") : Column "repunit" must be a character vector. It is not in reference data frame
I made sure to check before converting my genepop that repunit was a character vector by using this script :
repunits_reference = c("GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","NFL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL","GSL") as.character(repunits_reference) is.character(repunits_reference)
genepop_rubias(genepop = "/Volumes/drobo2/emilie_carrier/all_samples_fev_2019/03-bad_samples_high_relatedness_sex_removed/population_assignment_files/rubias/filtered_bad_samples_and_high_relatedness_removed_sex_removed_m4_p70_a0.01_A0.05_H0.6_one_snp_without_balancing_selection_baseline.gen", sampletype = "reference", repunits = repunits_reference, path = "/Volumes/drobo2/emilie_carrier/all_samples_fev_2019/03-bad_samples_high_relatedness_sex_removed/population_assignment_files/rubias/")
I tried running the example file from rubias to see if there was anything wrong with this package and it seems to work. Have you seen this problem before?
Thanks in advance!