remove quantile QTL code and other cleanup

.Rbuildignore

@@ -7,3 +7,4 @@
 ^pixi.lock
 ^\.pixi
 ^.covrignore
+^.claude

.github/recipe/recipe.yaml

@@ -30,8 +30,6 @@ requirements:
     - bioconductor-snpstats
     - r-base
     - r-bglr
-    - r-bigsnpr
-    - r-bigstatsr
     - r-coda
     - r-coloc
     - r-colocboost
@@ -44,6 +42,7 @@ requirements:
     - r-gbj
     - r-glmnet
     - r-harmonicmeanp
+    - r-igraph
     - r-l0learn
     - r-magrittr
     - r-mashr
@@ -54,8 +53,6 @@ requirements:
     - r-pgenlibr
     - r-purrr
     - r-qgg
-    - r-quadprog
-    - r-quantreg
     - r-rcpp
     - r-rcpparmadillo
     - r-rcppdpr
@@ -68,7 +65,6 @@ requirements:
     - r-tidyr
     - r-vctrs
     - r-vroom
-    - r-xicor
   run:
     - bioconductor-biostrings
     - bioconductor-iranges
@@ -77,8 +73,6 @@ requirements:
     - bioconductor-snpstats
     - r-base
     - r-bglr
-    - r-bigsnpr
-    - r-bigstatsr
     - r-coda
     - r-coloc
     - r-colocboost
@@ -91,6 +85,7 @@ requirements:
     - r-gbj
     - r-glmnet
     - r-harmonicmeanp
+    - r-igraph
     - r-l0learn
     - r-magrittr
     - r-mashr
@@ -101,8 +96,6 @@ requirements:
     - r-pgenlibr
     - r-purrr
     - r-qgg
-    - r-quadprog
-    - r-quantreg
     - r-rcpp
     - r-rcpparmadillo
     - r-rcppdpr
@@ -115,7 +108,6 @@ requirements:
     - r-tidyr
     - r-vctrs
     - r-vroom
-    - r-xicor
 
 tests:
   - script:

.gitignore

@@ -10,3 +10,4 @@ pecotmr.Rproj
 /pixi.lock
 /.pixi
 docs
+.claude

DESCRIPTION

@@ -18,13 +18,12 @@ Imports:
     IRanges,
     Rcpp,
     S4Vectors,
-    bigsnpr,
-    bigstatsr,
     coloc,
     doFuture,
     dplyr,
     furrr,
     future,
+    igraph,
     magrittr,
     matrixStats,
     purrr,
@@ -55,10 +54,6 @@ Suggests:
     ncvreg,
     pgenlibr,
     qgg,
-    quadprog,
-    quantreg,
-    udr,
-    XICOR,
     qvalue,
     rmarkdown,
     snpStats,
@@ -67,7 +62,6 @@ Remotes:
     stephenslab/fsusieR,
     stephenslab/mvsusieR,
     stephenslab/susieR,
-    stephenslab/udr
 LinkingTo:
     Rcpp,
     RcppArmadillo

NAMESPACE

@@ -1,7 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(QUAIL_pipeline)
-export(QUAIL_rank_score_pipeline)
 export(adjust_susie_weights)
 export(align_variant_names)
 export(allele_qc)
@@ -15,7 +13,6 @@ export(bayes_c_weights)
 export(bayes_l_weights)
 export(bayes_n_weights)
 export(bayes_r_weights)
-export(calculate_xi_correlation)
 export(check_ld)
 export(clean_context_names)
 export(coloc_post_processor)
@@ -58,7 +55,6 @@ export(load_multicontext_sumstats)
 export(load_multitask_regional_data)
 export(load_multitrait_R_sumstat)
 export(load_multitrait_tensorqtl_sumstat)
-export(load_quantile_twas_weights)
 export(load_regional_association_data)
 export(load_regional_functional_data)
 export(load_regional_multivariate_data)
@@ -79,8 +75,6 @@ export(mr_format)
 export(mrash_weights)
 export(mrmash_weights)
 export(mrmash_wrapper)
-export(multicontext_ld_clumping)
-export(multigene_udr)
 export(multivariate_analysis_pipeline)
 export(mvsusie_weights)
 export(normalize_variant_id)
@@ -89,11 +83,8 @@ export(otters_weights)
 export(parse_cs_corr)
 export(parse_region)
 export(parse_variant_id)
-export(perform_qr_analysis)
 export(prs_cs)
 export(prs_cs_weights)
-export(qr_screen)
-export(quantile_twas_weight_pipeline)
 export(raiss)
 export(read_afreq)
 export(region_to_df)
@@ -135,11 +126,8 @@ importFrom(IRanges,reduce)
 importFrom(IRanges,start)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
-importFrom(bigsnpr,snp_clumping)
-importFrom(bigstatsr,FBM.code256)
 importFrom(coloc,coloc.bf_bf)
 importFrom(doFuture,registerDoFuture)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
@@ -155,7 +143,9 @@ importFrom(dplyr,group_by)
 importFrom(dplyr,if_else)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,intersect)
+importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,row_number)
@@ -169,8 +159,8 @@ importFrom(future,availableCores)
 importFrom(future,multicore)
 importFrom(future,plan)
 importFrom(magrittr,"%>%")
+importFrom(matrixStats,colSds)
 importFrom(matrixStats,colVars)
-importFrom(parallel,mclapply)
 importFrom(purrr,compact)
 importFrom(purrr,exec)
 importFrom(purrr,map)
@@ -185,20 +175,14 @@ importFrom(readr,cols)
 importFrom(readr,parse_number)
 importFrom(readr,read_delim)
 importFrom(rlang,"!!!")
-importFrom(stats,as.dist)
 importFrom(stats,coef)
 importFrom(stats,cor)
-importFrom(stats,cov)
-importFrom(stats,cutree)
-importFrom(stats,hclust)
 importFrom(stats,lm.fit)
 importFrom(stats,pchisq)
 importFrom(stats,pnorm)
 importFrom(stats,predict)
-importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
-importFrom(stats,var)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_replace)
@@ -213,7 +197,6 @@ importFrom(susieR,susie_rss)
 importFrom(susieR,univariate_regression)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
-importFrom(tidyr,pivot_wider)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
 importFrom(tools,file_path_sans_ext)