Closed bschilder closed 2 years ago
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?
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.
CHANGES IN VERSION 1.3.1
New Features
import_sumstats
: Create individual folders for each GWAS dataset, with a respectivelogs
subfolder to avoid overwriting log files when processing multiple GWAS.parse_logs
: New function to convert logs from one or more munged GWAS into adata.table
.list_sumstats
: New function to recursively search for local summary stats files previously munged withMungeSumstats
.inst/extdata/MungeSumstats_log_msg.txt
to test logs files.list_sumstats
andparse_logs
.gh-pages
branch automatically by new GHA workflow.convert_large_p
andconvert_neg_p
, respectively. These are both handled by the new internal functioncheck_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 thecheck_range_p_val
step.check_small_p_val
now reports the number of SNPs <= 5e-324 to console/logs.check_range_p_val
andcheck_small_p_val
.parse_logs
can now extract information reported bycheck_range_p_val
andcheck_small_p_val
.logs_example
provides easy access to log file stored in inst/extdata, and includes documentation on how it was created.check_range_p_val
andcheck_small_p_val
now use#' @inheritParams format_sumstats
to improve consistency of documentation.Bug fixes
suppressWarnings
where possible.