minor fix the example

R/colocboost.R

@@ -107,13 +107,14 @@
 #' colnames(X) <- paste0("SNP", 1:P)
 #' L = 3
 #' true_beta <- matrix(0, P, L)
-#' true_beta[5, 1] <- 0.5  # SNP5 affects trait 1
-#' true_beta[5, 2] <- 0.4  # SNP5 also affects trait 2 (colocalized)
-#' true_beta[10, 2] <- 0.3 # SNP10 only affects trait 2
-#' true_beta[20, 3] <- 0.6 # SNP20 only affects trait 3
+#' true_beta[10, 1] <- 0.5  # SNP10 affects trait 1
+#' true_beta[10, 2] <- 0.4  # SNP10 also affects trait 2 (colocalized)
+#' true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
+#' true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
 #' Y <- matrix(0, N, L)
 #' for (l in 1:L){  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1) }
 #' res <- colocboost(X = X, Y = Y)
+#' res$cos_details$cos$cos_index
 #'
 #' @family colocboost
 #' @importFrom stats na.omit
@@ -551,7 +552,7 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
   if (min_variables < 100) {
     warning(
       "Warning message about the number of variables.\n",
-      "The smallest number of variables across outcomes is ", min_variables, "< 100.",
+      "The smallest number of variables across outcomes is ", min_variables, " < 100.",
       " If this is what you expected, this is not a problem.",
       " If this is not what you expected, please check input data."
     )

R/colocboost_output.R

@@ -34,10 +34,10 @@
 #' colnames(X) <- paste0("SNP", 1:P)
 #' L = 3
 #' true_beta <- matrix(0, P, L)
-#' true_beta[5, 1] <- 0.5  # SNP5 affects trait 1
-#' true_beta[5, 2] <- 0.4  # SNP5 also affects trait 2 (colocalized)
-#' true_beta[10, 2] <- 0.3 # SNP10 only affects trait 2
-#' true_beta[20, 3] <- 0.6 # SNP20 only affects trait 3
+#' true_beta[10, 1] <- 0.5  # SNP10 affects trait 1
+#' true_beta[10, 2] <- 0.4  # SNP10 also affects trait 2 (colocalized)
+#' true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
+#' true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
 #' Y <- matrix(0, N, L)
 #' for (l in 1:L){  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1) }
 #' res <- colocboost(X = X, Y = Y)
@@ -159,14 +159,16 @@ get_cos_summary <- function(cb_output,
 #' colnames(X) <- paste0("SNP", 1:P)
 #' L = 3
 #' true_beta <- matrix(0, P, L)
-#' true_beta[5, 1] <- 0.5  # SNP5 affects trait 1
-#' true_beta[5, 2] <- 0.4  # SNP5 also affects trait 2 (colocalized)
-#' true_beta[10, 2] <- 0.3 # SNP10 only affects trait 2
-#' true_beta[20, 3] <- 0.6 # SNP20 only affects trait 3
+#' true_beta[10, 1] <- 0.5  # SNP10 affects trait 1
+#' true_beta[10, 2] <- 0.4  # SNP10 also affects trait 2 (colocalized)
+#' true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
+#' true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
 #' Y <- matrix(0, N, L)
 #' for (l in 1:L){  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1) }
 #' res <- colocboost(X = X, Y = Y)
+#' res$cos_details$cos$cos_index
 #' filter_res <- get_strong_colocalization(res, cos_npc_cutoff = 0.5, npc_outcome_cutoff = 0.2)
+#' filter_res$cos_details$cos$cos_index
 #'
 #' @family colocboost_inference
 #' @export
@@ -472,10 +474,10 @@ get_ucos_summary <- function(cb_output, outcome_names = NULL, region_name = NULL
 #' colnames(X) <- paste0("SNP", 1:P)
 #' L = 3
 #' true_beta <- matrix(0, P, L)
-#' true_beta[5, 1] <- 0.5  # SNP5 affects trait 1
-#' true_beta[5, 2] <- 0.4  # SNP5 also affects trait 2 (colocalized)
-#' true_beta[10, 2] <- 0.3 # SNP10 only affects trait 2
-#' true_beta[20, 3] <- 0.6 # SNP20 only affects trait 3
+#' true_beta[10, 1] <- 0.5  # SNP10 affects trait 1
+#' true_beta[10, 2] <- 0.4  # SNP10 also affects trait 2 (colocalized)
+#' true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
+#' true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
 #' Y <- matrix(0, N, L)
 #' for (l in 1:L){  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1) }
 #' res <- colocboost(X = X, Y = Y)

R/colocboost_plot.R

@@ -45,14 +45,15 @@
 #' colnames(X) <- paste0("SNP", 1:P)
 #' L = 3
 #' true_beta <- matrix(0, P, L)
-#' true_beta[5, 1] <- 0.5  # SNP5 affects trait 1
-#' true_beta[5, 2] <- 0.4  # SNP5 also affects trait 2 (colocalized)
-#' true_beta[10, 2] <- 0.3 # SNP10 only affects trait 2
-#' true_beta[20, 3] <- 0.6 # SNP20 only affects trait 3
+#' true_beta[10, 1] <- 0.5  # SNP10 affects trait 1
+#' true_beta[10, 2] <- 0.4  # SNP10 also affects trait 2 (colocalized)
+#' true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
+#' true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
 #' Y <- matrix(0, N, L)
 #' for (l in 1:L){  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1) }
 #' res <- colocboost(X = X, Y = Y)
 #' colocboost_plot(res, plot_cols = 1)
+#' colocboost_plot(res, plot_cols = 1, outcome_idx = 1:3)
 #'
 #'
 #' @importFrom utils head tail

_pkgdown.yml

@@ -19,6 +19,23 @@ navbar:
     - icon: fa-github
       href: https://github.com/StatFunGen/colocboost
 
+articles:
+  - title: Vignettes
+    contents:
+    - Input_Data_Format
+    - Individual_Level_Colocalization
+    - Summary_Level_Colocalization
+    - ColocBoost_tutorial_basic
+    - ColocBoost_tutorial_advance
+    - ColocBoost_tutorial_GTEx
+    - ColocBoost_tutorial_strong_colocalization
+    - ColocBoost_tutorial_diagnostic
+
+  - title: internal
+    contents:
+    - announcements
+    - installation
+
 reference:
   - title: "Example Data"
     desc: "Example datasets for demonstration and testing"