From 7cdaa0a6def9e8d92d18c82609015b9e10791c2d Mon Sep 17 00:00:00 2001
From: leaffur <c.lin@yale.edu>
Date: Thu, 26 Jun 2025 00:54:29 -0400
Subject: [PATCH 1/2] Increment version number to 0.3.0

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3bce74c..a479035 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: CASE
 Title: Cell-type-specific And Shared EQTL fine-mapping
-Version: 0.2.3
+Version: 0.3.0
 Authors@R: c(
     person("Chen", "Lin", , "c.lin@yale.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9821-2578")),

From 9780f5344903dead43d0f68755405acb63458248 Mon Sep 17 00:00:00 2001
From: leaffur <c.lin@yale.edu>
Date: Thu, 26 Jun 2025 00:55:05 -0400
Subject: [PATCH 2/2] update verbose

---
 R/CASE.R                           |  2 +-
 man/CASE.Rd                        | 16 ++++++++++++++--
 man/CASE_test.Rd                   | 13 ++++++++++++-
 man/CASE_train.Rd                  | 13 ++++++++++++-
 man/get_credible_sets.Rd           |  3 +++
 vignettes/Introduction_to_CASE.Rmd |  2 ++
 6 files changed, 44 insertions(+), 5 deletions(-)

diff --git a/R/CASE.R b/R/CASE.R
index af25781..6cb96e2 100644
--- a/R/CASE.R
+++ b/R/CASE.R
@@ -88,7 +88,7 @@ CASE <- function(Z = NULL, R, hatB = NULL, hatS = NULL, N, V = NULL, cs = TRUE,
     t2 = Sys.time()
     res$time = difftime(t2, t1, units = "secs")
     if (cs){
-        res$sets <- get_credible_sets(res$pip, R = R, verbose = verbose)
+      res$sets <- get_credible_sets(res$pip, R = R, verbose = verbose)
     }
     
     return(res)
diff --git a/man/CASE.Rd b/man/CASE.Rd
index f84fa0c..d795f38 100644
--- a/man/CASE.Rd
+++ b/man/CASE.Rd
@@ -4,7 +4,17 @@
 \alias{CASE}
 \title{CASE}
 \usage{
-CASE(Z = NULL, R, hatB = NULL, hatS = NULL, N, V = NULL, cs = TRUE, ...)
+CASE(
+  Z = NULL,
+  R,
+  hatB = NULL,
+  hatS = NULL,
+  N,
+  V = NULL,
+  cs = TRUE,
+  verbose = TRUE,
+  ...
+)
 }
 \arguments{
 \item{Z}{M * C matrix of z scores.}
@@ -19,7 +29,9 @@ CASE(Z = NULL, R, hatB = NULL, hatS = NULL, N, V = NULL, cs = TRUE, ...)
 
 \item{V}{(optional) C * C covariance (correlation) matrix for the noise between traits. If not provided, the default is an identity matrix representing no correlations of the error.}
 
-\item{cs}{logical, whether to get credible sets.}
+\item{cs}{(optional) logical, whether to get credible sets. Default = TRUE.}
+
+\item{verbose}{(optional) logical, whether to print logging information. Default = TRUE.}
 
 \item{...}{additional arguments.}
 }
diff --git a/man/CASE_test.Rd b/man/CASE_test.Rd
index ef9b816..9107e73 100644
--- a/man/CASE_test.Rd
+++ b/man/CASE_test.Rd
@@ -4,7 +4,16 @@
 \alias{CASE_test}
 \title{CASE Model Testing}
 \usage{
-CASE_test(Z = NULL, R, hatB = NULL, hatS = NULL, N, CASE_training, ...)
+CASE_test(
+  Z = NULL,
+  R,
+  hatB = NULL,
+  hatS = NULL,
+  N,
+  CASE_training,
+  verbose = TRUE,
+  ...
+)
 }
 \arguments{
 \item{Z}{M * C matrix of z scores.}
@@ -19,6 +28,8 @@ CASE_test(Z = NULL, R, hatB = NULL, hatS = NULL, N, CASE_training, ...)
 
 \item{CASE_training}{A \code{"CASE_training"} object.}
 
+\item{verbose}{(optional) logical, whether to print logging information. Default = TRUE.}
+
 \item{...}{additional arguments.}
 }
 \value{
diff --git a/man/CASE_train.Rd b/man/CASE_train.Rd
index 318726d..9814ad3 100644
--- a/man/CASE_train.Rd
+++ b/man/CASE_train.Rd
@@ -4,7 +4,16 @@
 \alias{CASE_train}
 \title{CASE Model Training}
 \usage{
-CASE_train(Z = NULL, R, hatB = NULL, hatS = NULL, N, V = NULL, ...)
+CASE_train(
+  Z = NULL,
+  R,
+  hatB = NULL,
+  hatS = NULL,
+  N,
+  V = NULL,
+  verbose = TRUE,
+  ...
+)
 }
 \arguments{
 \item{Z}{M * C matrix of z scores.}
@@ -19,6 +28,8 @@ CASE_train(Z = NULL, R, hatB = NULL, hatS = NULL, N, V = NULL, ...)
 
 \item{V}{(optional) C * C covariance (correlation) matrix for the noise between traits. If not provided, the default is an identity matrix.}
 
+\item{verbose}{(optional) logical, whether to print logging information. Default = TRUE.}
+
 \item{...}{additional arguments.}
 }
 \value{
diff --git a/man/get_credible_sets.Rd b/man/get_credible_sets.Rd
index 985b433..611c54c 100644
--- a/man/get_credible_sets.Rd
+++ b/man/get_credible_sets.Rd
@@ -7,6 +7,7 @@
 get_credible_sets(
   pips,
   R,
+  verbose = TRUE,
   cor.min = 0.5,
   coverage_thres = 0.95,
   ruled_out = 1e-04
@@ -17,6 +18,8 @@ get_credible_sets(
 
 \item{R}{M * M matrix of LD.}
 
+\item{verbose}{(optional) logical, whether to print logging information. Default = TRUE.}
+
 \item{cor.min}{minimum correlation in the credible sets}
 
 \item{coverage_thres}{threshold for the sum of PIPs.}
diff --git a/vignettes/Introduction_to_CASE.Rmd b/vignettes/Introduction_to_CASE.Rmd
index d33cff8..a7ea260 100644
--- a/vignettes/Introduction_to_CASE.Rmd
+++ b/vignettes/Introduction_to_CASE.Rmd
@@ -27,6 +27,8 @@ set.seed(1000)
 
 ## The example data
 
+The example genotype was generated by R package `CorBin`.
+
 ```{r}
 data("example_data")
 attach(example_data)