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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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Strata error x Column `INDIVIDUALS` doesn't exist. #157

Closed didier-aurelle closed 2 years ago

didier-aurelle commented 2 years ago

Dear Thierry I try to import a vcf file with the tidy_genomic_data function as follows:

refuclim.vcf <- tidy_genomic_data(data = "refuclim_4_filter3.vcf", strata = "strata_refuclim_4_filter3.tsv")

I get this error, whereas I have an INDIVIDUALS column in my file and the right number of individuals

Execution date@time: 20220331@1546 Folder created: 02_radiator_tidy_genomic_20220331@1546 Function call and arguments stored in: radiator_tidy_genomic_data_args_20220331@1546.tsv Analyzing strata file Error in dplyr::select():
! Can't subset columns past the end. x Column INDIVIDUALS doesn't exist. Run rlang::last_error() to see where the error occurred.

the output of devtools::session_info():

─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.1.3 (2022-03-10) os Ubuntu 20.04.4 LTS system x86_64, linux-gnu ui RStudio language (EN) collate fr_FR.UTF-8 ctype fr_FR.UTF-8 tz Europe/Paris date 2022-03-31 rstudio 2021.09.1+372 Ghost Orchid (desktop) pandoc NA

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[1] /home/aurelle/R/x86_64-pc-linux-gnu-library/4.1 [2] /usr/local/lib/R/site-library [3] /usr/lib/R/site-library [4] /usr/lib/R/library

The data can be found here (zip file with vcf and strata files): https://amubox.univ-amu.fr/s/JjBjb7HJdW6SJbK

Thanks Didier

didier-aurelle commented 2 years ago

Sorry, I made an obvious mistake in my strata file, now it's corrected. I try to go further in the analysis, thanks