Merged
Conversation
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #469 +/- ##
===========================================
+ Coverage 27.48% 80.56% +53.08%
===========================================
Files 32 41 +9
Lines 4377 7760 +3383
===========================================
+ Hits 1203 6252 +5049
+ Misses 3174 1508 -1666 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
In this PR, I have attempted to fix the bottlenecks in enloc (this will need real testing).
I also wanted to clean up the sumstats QC pipeline which was kind of messy because dentist, for example had a whole other function which would load data separately from our main loading functions. I have now removed all functions which try to load data outside of our main pipeline.
The GCTA correction for LD estimation has been moved into R and is now available for compute_LD
These functions were removed, so we should figure out, where if anywhere, the xQTL pipeline could depend on them so it can be updated:
ctwas_bimfile_loader— loaded LD blocks from cTWAS bim files; replaced by ld_loader(LD_info=...)dentist_from_files— ran DENTIST end-to-end from file paths; replaced by composing load_genotype_region() + allele_qc() + compute_LD() + dentist()get_ctwas_meta_data— parsed cTWAS metadata; replaced by ld_loader(LD_info=...)parse_dentist_output— read output files from the DENTIST C++ binaryread_dentist_sumstat— read DENTIST-format summary statistics files