Mark legacy functions as internal and update pkgdown config

Author: bhattacharya-a-bt

.Rhistory

@@ -0,0 +1,6 @@
+pkgdown::build_site()
+pkgdown::build_site()
+pkgdown::preview_site(path='reference/univariate_elasticnet.html')
+pkgdown::build_site()
+devtools::document()
+pkgdown::build_site()

NAMESPACE

@@ -10,6 +10,8 @@ export(bayes_factor)
 export(burdenTest)
 export(burdenTest_all)
 export(compute_blup)
+export(compute_curds_whey)
+export(compute_finemap_regress)
 export(compute_fixed)
 export(compute_fixed_precomputed)
 export(compute_isotwas)
@@ -23,7 +25,9 @@ export(create_isotwas_model)
 export(create_isotwas_result)
 export(create_similarity_from_exons)
 export(create_transcript_model)
+export(curds_whey)
 export(estimate_cor)
+export(finemap_regress)
 export(get_prediction_matrix)
 export(get_resid)
 export(get_weight_matrix)
@@ -57,6 +61,7 @@ importFrom(boot,boot)
 importFrom(caret,createFolds)
 importFrom(condMVNorm,condMVN)
 importFrom(doParallel,registerDoParallel)
+importFrom(estimatr,lm_robust)
 importFrom(glmnet,cv.glmnet)
 importFrom(glmnet,glmnet)
 importFrom(huge,huge)
@@ -70,12 +75,15 @@ importFrom(rrBLUP,mixed.solve)
 importFrom(rtracklayer,import)
 importFrom(spls,cv.spls)
 importFrom(spls,spls)
+importFrom(stats,cancor)
 importFrom(stats,coef)
 importFrom(stats,cor.test)
 importFrom(stats,lm)
 importFrom(stats,model.matrix)
 importFrom(stats,pnorm)
+importFrom(stats,runif)
 importFrom(stats,sd)
+importFrom(susieR,susie)
 importFrom(tibble,tibble)
 importFrom(utils,combn)
 useDynLib(isotwas)

R/compute_curds_whey.R

@@ -21,6 +21,7 @@
 #' @importFrom rlist list.append
 #' @importFrom caret createFolds
 #'
+#' @keywords internal
 #' @export
 compute_curds_whey <- function(X,
                                Y,

R/compute_finemap_regress.R

@@ -21,6 +21,7 @@
 #' @importFrom tibble tibble
 #' @importFrom rlist list.append
 #'
+#' @keywords internal
 #' @export
 compute_finemap_regress <- function(X,
                                     Y,

R/compute_fixed.R

@@ -12,6 +12,7 @@
 #'
 #' @return list of MRCE estimates
 #'
+#' @keywords internal
 #' @export
 compute_fixed = function(X,
                          Y,
@@ -71,6 +72,7 @@ compute_fixed = function(X,
 #'
 #' @return list of MRCE estimates
 #'
+#' @keywords internal
 #' @export
 compute_fixed_precomputed = function(xtx,
                                      xtyom,

R/curds_whey.R

@@ -22,6 +22,7 @@
 #' @importFrom stats cancor
 #' @importFrom stats runif
 #'
+#' @keywords internal
 #' @export
 curds_whey <- function(X,
                        Y,

R/finemap_regress.R

@@ -17,6 +17,7 @@
 #' @importFrom susieR susie
 #' @importFrom estimatr lm_robust
 #'
+#' @keywords internal
 #' @export
 finemap_regress <- function(X,
                             Y,

_pkgdown.yml

@@ -67,3 +67,11 @@ reference:
       - bayes_factor
       - conditional_test_focus
       - conditional_test
+  - title: internal
+    contents:
+      - compute_curds_whey
+      - compute_finemap_regress
+      - compute_fixed
+      - compute_fixed_precomputed
+      - curds_whey
+      - finemap_regress