add ensemble TWAS

.github/recipe/recipe.yaml

@@ -56,9 +56,11 @@ requirements:
     - r-mr.mashr
     - r-mvsusier
     - r-ncvreg
+    - r-nnls
     - r-pgenlibr
     - r-purrr
     - r-qgg
+    - r-quadprog
     - r-rcppdpr
     - r-readr
     - r-rfast
@@ -98,6 +100,7 @@ requirements:
     - r-mr.mashr
     - r-mvsusier
     - r-ncvreg
+    - r-nnls
     - r-pgenlibr
     - r-purrr
     - r-qgg

DESCRIPTION

@@ -56,7 +56,9 @@ Suggests:
     mr.mashr,
     mvsusieR,
     ncvreg,
+    nnls,
     pgenlibr,
+    quadprog,
     qgg,
     qvalue,
     rmarkdown,

NAMESPACE

@@ -23,9 +23,13 @@ export(compute_qtl_enrichment)
 export(ctwas_bimfile_loader)
 export(dentist)
 export(dentist_single_window)
+export(dpr_adaptive_gibbs_weights)
+export(dpr_gibbs_weights)
+export(dpr_vb_weights)
 export(dpr_weights)
 export(enet_weights)
 export(enforce_design_full_rank)
+export(ensemble_weights)
 export(extract_cs_info)
 export(extract_flatten_sumstats_from_nested)
 export(extract_top_pip_info)
@@ -185,10 +189,12 @@ importFrom(readr,read_lines)
 importFrom(rlang,"!!!")
 importFrom(stats,as.dist)
 importFrom(stats,coef)
+importFrom(stats,complete.cases)
 importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,hclust)
 importFrom(stats,lm.fit)
+importFrom(stats,optim)
 importFrom(stats,pchisq)
 importFrom(stats,pnorm)
 importFrom(stats,predict)

R/regularized_regression.R

@@ -1208,3 +1208,15 @@ dpr_weights <- function(X, y, fitting_method = "VB", ...) {
   eff.wgt[keep] <- as.numeric(fit$beta + fit$alpha)
   return(eff.wgt)
 }
+
+#' @rdname dpr_weights
+#' @export
+dpr_vb_weights <- function(X, y, ...) dpr_weights(X, y, fitting_method = "VB", ...)
+
+#' @rdname dpr_weights
+#' @export
+dpr_gibbs_weights <- function(X, y, ...) dpr_weights(X, y, fitting_method = "Gibbs", ...)
+
+#' @rdname dpr_weights
+#' @export
+dpr_adaptive_gibbs_weights <- function(X, y, ...) dpr_weights(X, y, fitting_method = "Adaptive_Gibbs", ...)