RSS: drive univariate_rss.R through the current pecotmr camelCase API#1362
Closed
Yining97 wants to merge 1 commit into
Closed
RSS: drive univariate_rss.R through the current pecotmr camelCase API#1362Yining97 wants to merge 1 commit into
Yining97 wants to merge 1 commit into
Conversation
Port the modular RSS script off the removed snake API (rss_analysis_pipeline, load_study_LD, ...) to rssAnalysisPipeline/loadStudyLd with camelCase arguments so the protocol runs against current pecotmr. Move R_finite/R_mismatch into finemappingOpts, drop the unsupported init_L/max_L/l_step, map qc_method to zMismatchQc, expose --min-abs-corr / --median-abs-corr (threaded through the SoS notebook), coerce unset n-samples to 0, and fix two latent optparse parse_options bugs. Verified on chr21 AD_Bellenguez: runs end-to-end, matches a manual rssAnalysisPipeline call (ΔPIP=0), reproduces the step-1 result, and both purity thresholds reach susie_get_cs. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Contributor
Author
|
Superseded: pecotmr #524 removed rssAnalysisPipeline and replaced it with fineMappingPipeline()/GwasSumStats/summaryStatsQc(). Reworking against the new API on a fresh branch. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Port the modular RSS script off the removed snake API (rss_analysis_pipeline,
load_study_LD, ...) to rssAnalysisPipeline/loadStudyLd with camelCase arguments so
the protocol runs against current pecotmr. Move R_finite/R_mismatch into
finemappingOpts, drop the unsupported init_L/max_L/l_step, map qc_method to
zMismatchQc, expose --min-abs-corr / --median-abs-corr (threaded through the SoS
notebook), coerce unset n-samples to 0, and fix two latent optparse parse_options
bugs. Verified on chr21 AD_Bellenguez: runs end-to-end, matches a manual
rssAnalysisPipeline call (ΔPIP=0), reproduces the step-1 result, and both purity
thresholds reach susie_get_cs.
Co-Authored-By: Claude Opus 4.8 noreply@anthropic.com