From 53c862696590a3fb6b0fe5cf0c15974fb5265da5 Mon Sep 17 00:00:00 2001
From: hsun3163 <54919134+hsun3163@users.noreply.github.com>
Date: Fri, 11 Apr 2025 12:02:02 -0400
Subject: [PATCH 1/3] update interface of fsusie wrapper and the susiF function
 to reflect the newest run

---
 R/fsusie_wrapper.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/fsusie_wrapper.R b/R/fsusie_wrapper.R
index 28f2af3d..7e44bd59 100644
--- a/R/fsusie_wrapper.R
+++ b/R/fsusie_wrapper.R
@@ -118,7 +118,7 @@ fsusie_get_cs <- function(fSuSiE.obj, X, requested_coverage = 0.95) {
 #'         and without the dummy cs that do not meet the minimum purity requirement.
 #' @export
 
-fsusie_wrapper <- function(X, Y, pos, L, prior, max_SNP_EM, cov_lev, min.purity, max_scale, ...) {
+fsusie_wrapper <- function(X, Y, pos, L, prior, max_SNP_EM, cov_lev, min_purity, max_scale, ...) {
   # Make sure fsusieR installed
   if (!requireNamespace("fsusieR", quietly = TRUE)) {
     stop("To use this function, please install fsusieR: https://github.com/stephenslab/fsusieR")
@@ -127,11 +127,11 @@ fsusie_wrapper <- function(X, Y, pos, L, prior, max_SNP_EM, cov_lev, min.purity,
   fSuSiE.obj <- fsusieR::susiF(
     X = X, Y = Y, pos = pos, L = L, prior = prior,
     max_SNP_EM = max_SNP_EM, cov_lev = cov_lev,
-    min.purity = min.purity, max_scale = max_scale, ...
+    min_purity = min_purity, max_scale = max_scale, ...
   )
 
   # Remove dummy cs based on purity threshold
-  if (all(abs(as.numeric(fSuSiE.obj$purity)) < min.purity)) {
+  if (all(abs(as.numeric(fSuSiE.obj$purity)) < min_purity)) {
     fSuSiE.obj$cs <- list(NULL)
     fSuSiE.obj$sets <- list(cs = list(NULL), requested_coverage = cov_lev)
     fSuSiE.obj$cs_corr <- NULL # Set cs correlations to NULL if no credible sets meet purity criteria

From 83ee5244f6d8a038eb3f3db41295a63787a8c01c Mon Sep 17 00:00:00 2001
From: hsun3163 <54919134+hsun3163@users.noreply.github.com>
Date: Fri, 11 Apr 2025 12:03:06 -0400
Subject: [PATCH 2/3] Update fsusie_wrapper

---
 R/fsusie_wrapper.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/fsusie_wrapper.R b/R/fsusie_wrapper.R
index 7e44bd59..9a57fb04 100644
--- a/R/fsusie_wrapper.R
+++ b/R/fsusie_wrapper.R
@@ -112,7 +112,7 @@ fsusie_get_cs <- function(fSuSiE.obj, X, requested_coverage = 0.95) {
 #' @param cov_lev Coverage level for the credible sets.
 #' @param max_scale numeric, define the maximum of wavelet coefficients used in the analysis (2^max_scale).
 #'        Set 10 true by default.
-#' @param min.purity Minimum purity threshold for credible sets to be retained.
+#' @param min_purity Minimum purity threshold for credible sets to be retained.
 #' @param ... Additional arguments passed to the fsusie function.
 #' @return A modified fsusie object with the susie sets list, correlations for cs, alpha as df like susie,
 #'         and without the dummy cs that do not meet the minimum purity requirement.

From 57dd913a8414b218e1c3e8e8a7c33626e1d92016 Mon Sep 17 00:00:00 2001
From: hsun3163 <54919134+hsun3163@users.noreply.github.com>
Date: Fri, 11 Apr 2025 13:05:56 -0400
Subject: [PATCH 3/3] update the documentation of the new fsusie interface

---
 man/fsusie_wrapper.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/fsusie_wrapper.Rd b/man/fsusie_wrapper.Rd
index ab7ae724..09e9d71f 100644
--- a/man/fsusie_wrapper.Rd
+++ b/man/fsusie_wrapper.Rd
@@ -12,7 +12,7 @@ fsusie_wrapper(
   prior,
   max_SNP_EM,
   cov_lev,
-  min.purity,
+  min_purity,
   max_scale,
   ...
 )
@@ -32,7 +32,7 @@ fsusie_wrapper(
 
 \item{cov_lev}{Coverage level for the credible sets.}
 
-\item{min.purity}{Minimum purity threshold for credible sets to be retained.}
+\item{min_purity}{Minimum purity threshold for credible sets to be retained.}
 
 \item{max_scale}{numeric, define the maximum of wavelet coefficients used in the analysis (2^max_scale).
 Set 10 true by default.}