S4 refactor + feature additions (#493)

* add RSS extensions of MCP, SCAP, L0Learn

* add other p-value methods

* s4 refactor, h2 methods and pvalue combination methods

* LD cleanup

* rename some classes and clean up comments

* Update documentation

---------

Co-authored-by: danielnachun <danielnachun@users.noreply.github.com>

Author: danielnachun

.github/recipe/recipe.yaml

@@ -23,13 +23,20 @@ requirements:
     - ${{ stdlib('c') }}
     - ${{ compiler('cxx') }}
   host:
+    - bioconductor-biocparallel
+    - bioconductor-biostrings
+    - bioconductor-genomicranges
     - bioconductor-iranges
     - bioconductor-qvalue
     - bioconductor-s4vectors
     - bioconductor-snprelate
     - bioconductor-snpstats
     - bioconductor-mungesumstats
     - bioconductor-rsamtools
+    - bioconductor-rtracklayer
+    - bioconductor-summarizedexperiment
+    - r-arrow
+    - r-aspu
     - r-base
     - r-bglr
     - r-bigsnpr
@@ -39,26 +46,26 @@ requirements:
     - r-cpp11
     - r-cpp11armadillo
     - r-decor
-    - r-dofuture
     - r-dplyr
     - r-flashier
     - r-fsusier
-    - r-furrr
-    - r-future
     - r-gbj
     - r-glmnet
     - r-harmonicmeanp
     - r-igraph
     - r-l0learn
     - r-magrittr
     - r-mashr
+    - r-matrix
     - r-matrixstats
     - r-mr.ash.alpha
     - r-mr.mashr
     - r-mvsusier
     - r-ncvreg
     - r-nnls
     - r-pgenlibr
+    - r-plinkqc
+    - r-poolr
     - r-purrr
     - r-qgg
     - r-quadprog
@@ -73,42 +80,53 @@ requirements:
     - r-tidyr
     - r-vctrs
     - r-vroom
+    - r-xgboost
   run:
-    - bioconductor-biostrings
+    - bioconductor-biocparallel
+    - bioconductor-genomicranges
     - bioconductor-iranges
     - bioconductor-qvalue
     - bioconductor-s4vectors
+    - bioconductor-snprelate
     - bioconductor-snpstats
+    - bioconductor-mungesumstats
+    - bioconductor-rsamtools
+    - bioconductor-rtracklayer
+    - bioconductor-summarizedexperiment
+    - r-arrow
+    - r-aspu
     - r-base
     - r-bglr
     - r-bigsnpr
     - r-coda
     - r-coloc
     - r-colocboost
-    - r-dofuture
+    - r-cpp11
+    - r-cpp11armadillo
+    - r-decor
     - r-dplyr
     - r-flashier
     - r-fsusier
-    - r-furrr
-    - r-future
     - r-gbj
     - r-glmnet
     - r-harmonicmeanp
     - r-igraph
     - r-l0learn
     - r-magrittr
     - r-mashr
+    - r-matrix
     - r-matrixstats
     - r-mr.ash.alpha
     - r-mr.mashr
     - r-mvsusier
     - r-ncvreg
     - r-nnls
     - r-pgenlibr
+    - r-plinkqc
+    - r-poolr
     - r-purrr
     - r-qgg
-    - r-rcpp
-    - r-rcpparmadillo
+    - r-quadprog
     - r-rcppdpr
     - r-readr
     - r-rfast
@@ -120,6 +138,7 @@ requirements:
     - r-tidyr
     - r-vctrs
     - r-vroom
+    - r-xgboost
 
 tests:
   - script:

.gitignore

@@ -9,6 +9,7 @@ src/Makevars
 pecotmr.Rproj
 /pixi.lock
 /.pixi
+dev
 docs
 .claude
 dev

DESCRIPTION

@@ -14,18 +14,21 @@ Authors@R: c(person("Gao Wang",role = c("cre","aut"),
                   person("StatFunGen Lab", role = "ctb"))
 License: MIT + file LICENSE
 Imports:
+    BiocParallel,
+    Biostrings,
     GenomicRanges,
     IRanges,
+    MASS,
+    Matrix,
     MungeSumstats,
     Rsamtools,
     S4Vectors,
+    SummarizedExperiment,
     coloc,
-    doFuture,
     dplyr,
-    furrr,
-    future,
     magrittr,
     matrixStats,
+    methods,
     purrr,
     quadprog,
     readr,
@@ -38,35 +41,42 @@ Imports:
     vctrs,
     vroom
 Suggests:
+    aSPU,
+    arrow,
     BGLR,
     bigsnpr,
     bigstatsr,
     coda,
     colocboost,
-    GBJ,
-    L0Learn,
-    Rfast,
-    RcppDPR,
     flashier,
     fsusieR,
+    GBJ,
+    gdsfmt,
     glmnet,
     harmonicmeanp,
+    igraph,
     knitr,
+    L0Learn,
     lassosum,
     mashr,
     mr.mashr,
     mvsusieR,
     ncvreg,
     nnls,
     pgenlibr,
+    plinkQC,
+    poolr,
     qgg,
     qvalue,
+    Rfast,
+    RcppDPR,
     rmarkdown,
-    gdsfmt,
+    rtracklayer,
     SNPRelate,
     snpStats,
     testthat,
-    VariantAnnotation
+    VariantAnnotation,
+    xgboost
 Remotes:
     stephenslab/fsusieR,
     stephenslab/mvsusieR,
@@ -78,3 +88,48 @@ NeedsCompilation: yes
 VignetteBuilder: knitr
 Config/roxygen2/version: 8.0.0
 RoxygenNote: 7.3.3
+Collate:
+    'AllClasses.R'
+    'AllGenerics.R'
+    'AllMethods.R'
+    'LD.R'
+    'allele_qc.R'
+    'colocboost_pipeline.R'
+    'compute_qtl_enrichment.R'
+    'cpp11.R'
+    'ctwas_wrapper.R'
+    'dentist_qc.R'
+    'encoloc.R'
+    'example_data.R'
+    'file_utils.R'
+    'fsusie_wrapper.R'
+    'genotype_io.R'
+    'gwas_sumstats.R'
+    'h2_annotations.R'
+    'h2_estimate_wrappers.R'
+    'h2_gldsc.R'
+    'h2_hdl.R'
+    'h2_lder.R'
+    'h2_utils.R'
+    'ld_loader.R'
+    'mash_wrapper.R'
+    'misc.R'
+    'mr.R'
+    'mrmash_wrapper.R'
+    'multitrait_data.R'
+    'multivariate_pipeline.R'
+    'otters.R'
+    'pval_combine.R'
+    'raiss.R'
+    'regularized_regression.R'
+    'relatedness_qc.R'
+    'slalom.R'
+    'sldsc_wrapper.R'
+    'sumstats_qc.R'
+    'susie_wrapper.R'
+    'twas.R'
+    'twas_weights.R'
+    'univariate_pipeline.R'
+    'univariate_rss_diagnostics.R'
+    'variant_id.R'
+    'vcf_writer.R'