Bschilder dev

[bschilder]

CHANGES IN VERSION 1.3.1

New Features

• import_sumstats: Create individual folders for each GWAS dataset, with a respective logs subfolder to avoid overwriting log files when processing multiple GWAS.
• parse_logs: New function to convert logs from one or more munged GWAS into a data.table.
• list_sumstats: New function to recursively search for local summary stats files previously munged with MungeSumstats.
• Added new dataset inst/extdata/MungeSumstats_log_msg.txt to test logs files.
• Added unit tests for list_sumstats and parse_logs.
• Added new Docker vignette.
• Updated GHA workflows using r_workflows.
• Remove docs/ folder as the website will now be pushed to the gh-pages branch automatically by new GHA workflow.
• Made documentation in README more clear and concise.
• Added checks for p-values >1 or <0 via args convert_large_p and convert_neg_p, respectively. These are both handled by the new internal function check_range_p_val, which also reports the number of SNPs found meeting these criteria to the console/logs.
• check_small_p_val records which SNPs were imputed in a more robust way, by recording which SNPs met the criteria before making the changes (as opposed to inferred this info from which columns are 0 after making the changes). This function now only handles non-negative p-values, so that rows with negative p-values can be recorded/reported separately in the check_range_p_val step.
• check_small_p_val now reports the number of SNPs <= 5e-324 to console/logs.
• Unit tests have been added for both check_range_p_val and check_small_p_val.
• parse_logs can now extract information reported by check_range_p_val and check_small_p_val.
• New internal function logs_example provides easy access to log file stored in inst/extdata, and includes documentation on how it was created.
• Both check_range_p_val and check_small_p_val now use #' @inheritParams format_sumstats to improve consistency of documentation.

Bug fixes

• Reduced vignette sizes.
• Removed usage of suppressWarnings where possible.
• Deleted old .Rproj file and hidden folder (contained large files).
• Configured .Rproj so it doesn't store large data files.

[Al-Murphy]

Still errors appearing in the GHA checks. IS this something you will get some time to investigate do you think? Have you encountered errors in GHA's like these before with your solution?

[bschilder]

Still errors appearing in the GHA checks. IS this something you will get some time to investigate do you think? Have you encountered errors in GHA's like these before with your solution?

Dang, no these are new. Not sure what these error messages mean but I'll try to investigate today.