S4 refactor + feature additions

[danielnachun]

In this PR I am adding the last remaining missing features for now:

• some alternatives for p-value combination for TWAS
• some extra RSS methods for LASSO (MCP, SCAD and L0Learn)
• stratified LDSC, LDER and HDL - assumes the use has the baseline model annotations

One important caveat to the LDSC/LDER/HDL implementations is that several of the baseline model annotations are dependent on the population but require a demographic model, recombination map, variant ages and selection coefficients. The ecosystem of packages I'm developing will eventually provide the user with the option to estimate all of the necessary quantities from the same genotype data so that it will eventually be possible for the user to only need to provide the functional annotation parts of the baseline model, but that is for a later time.

The other large refactoring is the implementation of S4 classes. Surprisingly so far this has very minimal impact on the user interface - the only anticipated breakage is for the TWAS parts of the xQTL pipeline that are being moved to pecotmr anyway.

[codecov]

Codecov Report

❌ Patch coverage is 82.16712% with 525 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.15%. Comparing base (c638868) to head (0a817eb).

Files with missing lines	Patch %	Lines
R/mash_wrapper.R	3.52%	137 Missing ⚠️
R/genotype_io.R	78.51%	55 Missing ⚠️
R/misc.R	66.92%	42 Missing ⚠️
R/h2_gldsc.R	82.58%	35 Missing ⚠️
R/LD.R	48.48%	34 Missing ⚠️
R/allele_qc.R	3.03%	32 Missing ⚠️
R/mrmash_wrapper.R	0.00%	24 Missing ⚠️
R/gwas_sumstats.R	79.38%	20 Missing ⚠️
R/relatedness_qc.R	81.37%	19 Missing ⚠️
R/h2_hdl.R	91.17%	18 Missing ⚠️
... and 19 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #493      +/-   ##
==========================================
+ Coverage   82.95%   86.15%   +3.19%     
==========================================
  Files          36       52      +16     
  Lines        9130    11614    +2484     
==========================================
+ Hits         7574    10006    +2432     
- Misses       1556     1608      +52     

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