Add new GWAS calculation in the Tool "Check your phenotype"

[VincentGardeux]

In http://biccsrv3.epfl.ch:32786/check_pheno We need to add the new GWAS calculation.

Also, we need to add the gene enrichment results. We have two options:

• 1. Keeping it within the main R script (it makes a system call to a Python script). This will increase a lot the time it takes to run.
• 2. Getting it out of the main R script. Then the script will still take ~1mn30 to run, but then we need to call the 2 Python scripts outside. And make sure we don't overload the server...

[VincentGardeux]

To check:

• list of required R packages: data.table, stringr, ramwas, car, rstatix, Cairo, jsonlite
• Default value for param 7: 0.2
• Default value for param 8: 0.01
• New param at pos 9: filtering p-value threshold. Should be 0.001 by default. The old optional param that was at pos 9 is now at pos 10
• Categorical phenotypes should now fail with an error message
• Output covariate file should now contain Shapiro + Kruskal results
• Output JSON file should now contain the exact command line that is ran: command_line_gwas. We should maybe display it somewhere?
• I now use CairoPDF for generating the PDFs. They should be less bugged.
• I now generate two output files for the GWAS: *.fdr.annot.tsv.gz containing all results (in JSON hash plink_output_file) and .top_{filtering_pval}.annot.tsv.gz containing the filtered results, at p-value threshold in param 9 (in JSON hash plink_filtered_output_file)

[fab-dav]

6. [Required] Number of threads

7. [Required] Minimum genotyping ratio

8. [Required] Minimum MAF

9. [Required] Filtering threshold for p-value