Doc fixes

R/colocboost.R

@@ -51,7 +51,7 @@
 #' @param jk_equiv_corr The LD cutoff between overall best update jk-star and marginal best update jk-l for lth outcome
 #' @param jk_equiv_loglik The change of loglikelihood cutoff between overall best update jk-star and marginal best update jk-l for lth outcome
 #' @param coloc_thresh The cutoff of checking if the best update jk-star is the potential causal variable for outcome l if jk-l is not similar to jk-star (used in Delayed SEC).
-#' @param lambda The ratio [0,1] for z^2 and z in fun_prior simplex, defult is 0.5
+#' @param lambda The ratio \[0,1\] for z^2 and z in fun_prior simplex, defult is 0.5
 #' @param lambda_target_outcome The ratio for z^2 and z in fun_prior simplex for the target outcome, default is 1
 #' @param func_simplex The data-driven local association simplex \eqn{\delta} for smoothing the weights. Default is "LD_z2z" is the elastic net for z-score and also weighted by LD.
 #' @param func_multi_test The alternative method to check the stop criteria. When \code{func_multi_test = "lfdr"}, boosting iterations will be stopped
@@ -98,10 +98,7 @@
 #'
 #' @importFrom stats na.omit
 #' @export
-#'
-#' @examples
-#' colocboost(X=X, Y=Y)
-#'
+
 colocboost <- function(X = NULL, Y = NULL, # individual data
                        sumstat = NULL, LD = NULL, # summary statistics: either Z, bhat, sebhat, N, var_Y,
                        ###### - index dict for X match multiple Y / LD match multiple sumstat

R/colocboost_output.R

@@ -23,10 +23,6 @@
 #' \item{colocalized_variables}{List of colocalized variables}
 #' \item{colocalized_variables_vcp}{Variant colocalization probabilities for all colocalized variables}
 #'
-#' @examples
-#' get_cos_summary(cb_output)
-#' get_cos_summary(cb_output, interest_outcome = c("Y1", "Y2"))
-#'
 #' @keywords cb_get_functions
 #' @export
 get_cos_summary <- function(cb_output, 
@@ -124,9 +120,6 @@ get_cos_summary <- function(cb_output,
 #' \item{data_info}{A object with detailed information from input data}
 #' \item{model_info}{A object with detailed information for colocboost model}
 #'
-#' @examples
-#' get_strong_colocalization(cb_output, cos_npc_cutoff = 0.5, npc_outcome_cutoff = 0.25)
-#'
 #' @keywords cb_get_functions
 #' @export
 get_strong_colocalization <- function(cb_output, 
@@ -359,9 +352,6 @@ get_strong_colocalization <- function(cb_output,
 #' \item{ucos_variables}{List of fine-mapped variables}
 #' \item{ucos_variables_pip}{Posterior inclusion probability (PIP) for all fine-mapped variables}
 #'
-#' @examples
-#' get_ucos_summary(cb_output)
-#'
 #' @keywords cb_get_functions
 #' @noRd
 get_ucos_summary <- function(cb_output, outcome_names = NULL, gene_name = NULL){

R/colocboost_plot.R

@@ -38,9 +38,6 @@
 #' @importFrom graphics abline axis legend mtext par points text
 #' @importFrom grDevices adjustcolor
 #' 
-#' @examples
-#' colocboost_plot(cb_output)
-#'
 #' @keywords cb_plot
 #' @export
 colocboost_plot <- function(cb_output, y = "log10p", 

R/colocboost_utils.R

@@ -472,5 +472,3 @@ get_merge_ordered_with_indices <- function(vector_list) {
 
   result
 }
-
-

R/data.R

@@ -0,0 +1,27 @@
+#' Individual level data for 5 traits
+#'
+#' An example dataset with simulated genotypes and outcomes for 5 traits
+#'
+#' @format ## `Ind_5traits`
+#' A list with 3 elements
+#' \describe{
+#'   \item{X}{List of genotype matrices}
+#'   \item{Y}{List of outcomes}
+#'   \item{TrueCausalVariants}{List of causal variants}
+#' }
+#' @source FINISH
+"Ind_5traits"
+
+#' Summary level data for 5 traits
+#'
+#' An example dataset with simulated statistics and LD for 5 traits
+#'
+#' @format ## `Sumstat_5traits`
+#' A list with 3 elements
+#' \describe{
+#'   \item{sumstat}{Summary statistics for 5 traits}
+#'   \item{LD}{Matrix of LD between variants}
+#'   \item{TrueCausalVariants}{List of causal variants}
+#' }
+#' @source FINISH
+"Sumstat_5traits"

tests/testthat.R

@@ -9,4 +9,4 @@
 library(testthat)
 library(colocboost)
 
-test_check("colocboost")
+test_check("colocboost")

tests/testthat/test_utils.R

@@ -181,4 +181,4 @@ test_that("get_merge_ordered_with_indices merges vectors", {
   vector_list2 <- list(vec1, vec1, vec2, vec3)
   result2 <- get_merge_ordered_with_indices(vector_list2)
   expect_equal(result2, c("a", "b", "c", "d", "e"))
-})
+})