thierrygosselin
commented
4 months ago That internal function is deprecated and no longer used, try uninstalling radiator and grur and reinstalling it.
Not that it matters but it was replaced by generate_stats that handle both individuals and markers stats.
Re-open the issue if you're still experiencing a problem.
Dear thierrygosselin,
I installed "grur" and "radiator" in R in my Ubuntu environment and I used filter_rad successfully same file before. But when i used "missing_visualization" to check my missing data visually, error was occured.
error message "Error: 'generate_id_stats' is not an exported object from 'namespace:radiator'"was shown again and again.
This error looks same issues which is not solved yet of issue at Grur "https://github.com/thierrygosselin/grur/issues/16"
I use 1.3.0 version of radiator and 0.1.4 version of grur
The entire output I got is below
missing_visualization function call arguments: data = populations.snps.vcf strata = my.strata.tsv strata.select = POP_ID distance.method = euclidean ind.missing.geno.threshold = 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90 filename = NULL parallel.core = 7 write.plot = TRUE
Default "..." arguments assigned in missing_visualization: path.folder = NULL
Folder created: missing_visualization_20240325@1426 File written: grur_missing_visualization_data_args_20240325@1426.tsv
Importing data ✔ Reading VCF... you might have time for an espresso! [1m 1.4s]
Cleaning VCF
Filter monomorphic markers Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 4 / 25245 / 54184
Filter common markers: Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 7 / 36175 / 83056
VCF info: Number of chromosome/contig/scaffold: 105 Number of locus: 257576 Number of markers: 541867 Number of strata: 6 Number of individuals: 288
Number of ind/strata: SEW = 48 GTL = 55 LEM = 47 STR = 41 FIN = 48 GEL = 49
Number of duplicate id: 0 radiator Genomic Data Structure (GDS) file: radiator_20240325@1426.gds Error: 'generate_id_stats' is not an exported object from 'namespace:radiator'
Computation time, overall: 150 sec ############################ missing_visualization #############################