From b10d89394eb938c628dba49c2f77ee92f4bd3055 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:23:52 -0400
Subject: [PATCH 1/7] minor fix

---
 vignettes/LD_Free_Colocalization.Rmd            | 15 ++++++++++++---
 vignettes/Summary_Statistics_Colocalization.Rmd | 14 +++++++++++---
 2 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index aa58ee4..66bc414 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -129,13 +129,22 @@ for (i in 1:length(X)){
   x <- X[[i]]
   y <- Y[[i]]
   effect_n[i] <- length(y)
-  rr <- susieR::univariate_regression(X = x, y = y)
-  effect_est <- cbind(effect_est, rr$betahat)
-  effect_se <- cbind(effect_se, rr$sebetahat)
+  # simple usiing `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]))$coef
+    if (nrow(fit) == 2)
+      output[i,] = as.vector(summary(lm(y ~ X[,i]))$coef[2,1:2])
+    else
+      output[i,] = c(0,0)
+  }
+  effect_est <- cbind(effect_est, output[,1])
+  effect_se <- cbind(effect_se, output[,2])
 }
 colnames(effect_est) <- colnames(effect_se) <- c("Y1", "Y2", "Y3", "Y4", "Y5")
 rownames(effect_est) <- rownames(effect_se) <- colnames(X[[1]])
 
+
 # Run colocboost
 res <- colocboost(effect_est = effect_est, effect_se = effect_se, effect_n = effect_n)
 
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index 17dcaba..f3488bd 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -189,9 +189,17 @@ for (i in 1:length(X)){
   x <- X[[i]]
   y <- Y[[i]]
   effect_n[i] <- length(y)
-  rr <- susieR::univariate_regression(X = x, y = y)
-  effect_est <- cbind(effect_est, rr$betahat)
-  effect_se <- cbind(effect_se, rr$sebetahat)
+  # simple usiing `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]))$coef
+    if (nrow(fit) == 2)
+      output[i,] = as.vector(summary(lm(y ~ X[,i]))$coef[2,1:2])
+    else
+      output[i,] = c(0,0)
+  }
+  effect_est <- cbind(effect_est, output[,1])
+  effect_se <- cbind(effect_se, output[,2])
 }
 colnames(effect_est) <- colnames(effect_se) <- c("Y1", "Y2", "Y3", "Y4", "Y5")
 rownames(effect_est) <- rownames(effect_se) <- colnames(X[[1]])

From 8d2162fa33ca3b6e82571363aa2c90f9ff67b65f Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:25:45 -0400
Subject: [PATCH 2/7] Update CITATION

---
 inst/CITATION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/CITATION b/inst/CITATION
index 34719dc..9cb21d5 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -6,7 +6,7 @@ citEntry(
   author   = c(person("Xuewei", "Cao"),
                person("Haochen", "Sun"),
                person("Ru", "Feng"),
-               person("Rajib", "Mazumder"),
+               person("Rahul", "Mazumder"),
                person("Cristian F. B.", "Najar"),
                person("Yang I.", "Li"),
                person("Philip L.", "de Jager"),

From 0de97f148ad5ba67777203c846437a3031319210 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:26:31 -0400
Subject: [PATCH 3/7] Update Summary_Statistics_Colocalization.Rmd

---
 vignettes/Summary_Statistics_Colocalization.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index f3488bd..e2e33b5 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -190,7 +190,7 @@ for (i in 1:length(X)){
   y <- Y[[i]]
   effect_n[i] <- length(y)
   # simple usiing `rr <- susieR::univariate_regression(X = x, y = y)`
-  output = matrix(0,ncol(X),2)
+  output = matrix(0,ncol(x),2)
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef
     if (nrow(fit) == 2)

From 1b8b74ecd16e42a68e6b16453f26ab66b82922f8 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:26:40 -0400
Subject: [PATCH 4/7] Update LD_Free_Colocalization.Rmd

---
 vignettes/LD_Free_Colocalization.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index 66bc414..1922438 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -130,7 +130,7 @@ for (i in 1:length(X)){
   y <- Y[[i]]
   effect_n[i] <- length(y)
   # simple usiing `rr <- susieR::univariate_regression(X = x, y = y)`
-  output = matrix(0,ncol(X),2)
+  output = matrix(0,ncol(x),2)
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef
     if (nrow(fit) == 2)

From 7015622db0ab5a6132c181d4e79e035d2842b394 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:29:46 -0400
Subject: [PATCH 5/7] fix

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

diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index 1922438..064a6f5 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -134,7 +134,7 @@ for (i in 1:length(X)){
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef
     if (nrow(fit) == 2)
-      output[i,] = as.vector(summary(lm(y ~ X[,i]))$coef[2,1:2])
+      output[i,] = as.vector(fit$coef[2,1:2])
     else
       output[i,] = c(0,0)
   }
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index e2e33b5..59438ea 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -194,7 +194,7 @@ for (i in 1:length(X)){
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef
     if (nrow(fit) == 2)
-      output[i,] = as.vector(summary(lm(y ~ X[,i]))$coef[2,1:2])
+      output[i,] = as.vector(fit$coef[2,1:2])
     else
       output[i,] = c(0,0)
   }

From d2bcc4866f829d2935933db94a81af8fcc735e4f Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:33:30 -0400
Subject: [PATCH 6/7] fix

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

diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index 064a6f5..fd6b1e1 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -134,7 +134,7 @@ for (i in 1:length(X)){
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef
     if (nrow(fit) == 2)
-      output[i,] = as.vector(fit$coef[2,1:2])
+      output[i,] = as.vector(fit[2,1:2])
     else
       output[i,] = c(0,0)
   }
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index 59438ea..278eabd 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -194,7 +194,7 @@ for (i in 1:length(X)){
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef
     if (nrow(fit) == 2)
-      output[i,] = as.vector(fit$coef[2,1:2])
+      output[i,] = as.vector(fit[2,1:2])
     else
       output[i,] = c(0,0)
   }

From 6f15847d92e4b0b3a4971ccdfde90602e1c12432 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sun, 20 Apr 2025 20:37:39 -0400
Subject: [PATCH 7/7] fix

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

diff --git a/vignettes/LD_Free_Colocalization.Rmd b/vignettes/LD_Free_Colocalization.Rmd
index fd6b1e1..8a616b6 100644
--- a/vignettes/LD_Free_Colocalization.Rmd
+++ b/vignettes/LD_Free_Colocalization.Rmd
@@ -129,7 +129,7 @@ for (i in 1:length(X)){
   x <- X[[i]]
   y <- Y[[i]]
   effect_n[i] <- length(y)
-  # simple usiing `rr <- susieR::univariate_regression(X = x, y = 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]))$coef
diff --git a/vignettes/Summary_Statistics_Colocalization.Rmd b/vignettes/Summary_Statistics_Colocalization.Rmd
index 278eabd..1ddd97e 100644
--- a/vignettes/Summary_Statistics_Colocalization.Rmd
+++ b/vignettes/Summary_Statistics_Colocalization.Rmd
@@ -189,7 +189,7 @@ for (i in 1:length(X)){
   x <- X[[i]]
   y <- Y[[i]]
   effect_n[i] <- length(y)
-  # simple usiing `rr <- susieR::univariate_regression(X = x, y = y)`
+  # simply use `rr <- susieR::univariate_regression(X = x, y = y)`
   output = matrix(0,ncol(x),2)
   for (i in 1:ncol(x)) {
     fit = summary(lm(y ~ x[,i]))$coef