From 5f1abdf9bc39f84e84f54a8ec97e38afbce86958 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Tue, 22 Apr 2025 19:07:28 -0400
Subject: [PATCH 1/2] adding susieR

---
 DESCRIPTION                                     |  3 ++-
 vignettes/Ambiguous_Colocalization.Rmd          |  7 +++++++
 vignettes/LD_Free_Colocalization.Rmd            | 10 +---------
 vignettes/Summary_Statistics_Colocalization.Rmd | 10 +---------
 4 files changed, 11 insertions(+), 19 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 72ab83e..b427df5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,8 @@ Suggests:
     knitr,
     rmarkdown,
     ashr,
-    MASS
+    MASS,
+    susieR
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
diff --git a/vignettes/Ambiguous_Colocalization.Rmd b/vignettes/Ambiguous_Colocalization.Rmd
index c9b3995..b056ac8 100644
--- a/vignettes/Ambiguous_Colocalization.Rmd
+++ b/vignettes/Ambiguous_Colocalization.Rmd
@@ -105,6 +105,13 @@ susie_GWAS$sets$cs$L1
 intersect(susie_eQTL$sets$cs$L1, susie_GWAS$sets$cs$L1)
 ```
 
+To visulize the fine-mapping results,
+
+```{r plot-susie}
+susieR::susie_plot(susie_eQTL, y = "PIP")
+susieR::susie_plot(susie_GWAS, y = "PIP")
+```
+
 
 # 3. Get the ambiguous colocalization results and summary
 
diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index ae67414..9cba14a 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -131,15 +131,7 @@ for (i in 1:length(X)){
   x <- X[[i]]
   y <- Y[[i]]
   effect_n[i] <- length(y)
-  # simply use `rr <- susieR::univariate_regression(X = x, y = y)`
-  output = matrix(0,ncol(x),2)
-  for (i in 1:ncol(x)) {
-    fit = summary(lm(y ~ x[,i]))$coef
-    if (nrow(fit) == 2)
-      output[i,] = as.vector(fit[2,1:2])
-    else
-      output[i,] = c(0,0)
-  }
+  output <- susieR::univariate_regression(X = x, y = y)
   effect_est <- cbind(effect_est, output[,1])
   effect_se <- cbind(effect_se, output[,2])
 }
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index 304b6bf..311916b 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -190,15 +190,7 @@ for (i in 1:length(X)){
   x <- X[[i]]
   y <- Y[[i]]
   effect_n[i] <- length(y)
-  # simply use `rr <- susieR::univariate_regression(X = x, y = y)`
-  output = matrix(0,ncol(x),2)
-  for (i in 1:ncol(x)) {
-    fit = summary(lm(y ~ x[,i]))$coef
-    if (nrow(fit) == 2)
-      output[i,] = as.vector(fit[2,1:2])
-    else
-      output[i,] = c(0,0)
-  }
+  output <- susieR::univariate_regression(X = x, y = y)
   effect_est <- cbind(effect_est, output[,1])
   effect_se <- cbind(effect_se, output[,2])
 }

From 9e0cb6ea0e546da346202ca57c085ce2d2f5a48d Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Tue, 22 Apr 2025 19:15:04 -0400
Subject: [PATCH 2/2] minor fix

---
 vignettes/LD_Free_Colocalization.Rmd            | 4 ++--
 vignettes/Summary_Statistics_Colocalization.Rmd | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index 9cba14a..75aaf81 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -132,8 +132,8 @@ for (i in 1:length(X)){
   y <- Y[[i]]
   effect_n[i] <- length(y)
   output <- susieR::univariate_regression(X = x, y = y)
-  effect_est <- cbind(effect_est, output[,1])
-  effect_se <- cbind(effect_se, output[,2])
+  effect_est <- cbind(effect_est, output$beta)
+  effect_se <- cbind(effect_se, output$sebeta)
 }
 colnames(effect_est) <- colnames(effect_se) <- c("Y1", "Y2", "Y3", "Y4", "Y5")
 rownames(effect_est) <- rownames(effect_se) <- colnames(X[[1]])
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index 311916b..4e4f8da 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -191,8 +191,8 @@ for (i in 1:length(X)){
   y <- Y[[i]]
   effect_n[i] <- length(y)
   output <- susieR::univariate_regression(X = x, y = y)
-  effect_est <- cbind(effect_est, output[,1])
-  effect_se <- cbind(effect_se, output[,2])
+  effect_est <- cbind(effect_est, output$beta)
+  effect_se <- cbind(effect_se, output$sebeta)
 }
 colnames(effect_est) <- colnames(effect_se) <- c("Y1", "Y2", "Y3", "Y4", "Y5")
 rownames(effect_est) <- rownames(effect_se) <- colnames(X[[1]])