TWAS pipeline refactor and full S4 refactor

[danielnachun]

This PR should greatly clean up our TWAS pipeline:

• Now we use eigenvectors and eigenvalues of the LD sketch to compute Z scores instead of computing a full R matrix
• The OTTERS pipeline has been renamed and made into a generic summary-based TWAS pipeline - it also uses our RSS QC machinery on the eQTL sumstats
• Colocalization with coloc and encoloc now can redo GWAS fine-mapping results in the gene window, though genome-wide fine-mapping must be run in advance for encoloc to get its priors
• Data structures now use S4 classes wherever possible. This is probably not the last cleanup for this but is a huge step in the right direction.

[codecov]

Codecov Report

❌ Patch coverage is 77.29124% with 223 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.43%. Comparing base (3267a8a) to head (7dc0e53).

Files with missing lines	Patch %	Lines
R/twas_weights.R	65.38%	63 Missing ⚠️
R/twas.R	81.00%	57 Missing ⚠️
R/file_utils.R	67.74%	30 Missing ⚠️
R/encoloc.R	80.20%	19 Missing ⚠️
R/LD.R	72.00%	14 Missing ⚠️
R/sumstats_qc.R	76.00%	12 Missing ⚠️
R/regularized_regression.R	66.66%	8 Missing ⚠️
R/AllMethods.R	69.56%	7 Missing ⚠️
R/variant_id.R	92.30%	3 Missing ⚠️
R/ld_loader.R	50.00%	2 Missing ⚠️
... and 7 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #501      +/-   ##
==========================================
- Coverage   86.26%   85.43%   -0.83%     
==========================================
  Files          52       51       -1     
  Lines       11619    12091     +472     
==========================================
+ Hits        10023    10330     +307     
- Misses       1596     1761     +165     

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