From 52e4c0368d1d4f33ef38b86ca84cac4293cc3305 Mon Sep 17 00:00:00 2001
From: Chen Weng <43254272+chenweng1991@users.noreply.github.com>
Date: Wed, 25 Oct 2023 15:23:55 -0400
Subject: [PATCH] Update BuidTree.R

Fix compatibility with Seurat v5
in SeuratLSIClustering
---
 R/BuidTree.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/BuidTree.R b/R/BuidTree.R
index 213d602..438593a 100755
--- a/R/BuidTree.R
+++ b/R/BuidTree.R
@@ -246,7 +246,12 @@ setMethod(f="SeuratLSIClustering",
           signature="redeemR",
           definition=function(object,binary=T,res=0.6,lsidim=2:50,rmvariants=c("Variants310TC","Variants3109TC","Variants5764CT")){
           require(Signac)
+          require(Seurat)
           if(binary){
+              if (packageVersion("Seurat")>"4.9.9"){
+                  print("Seurat5 is on, convert data structure to v4")
+                  options(Seurat.object.assay.version = 'v4')
+              }
               Cts.Mtx.bi<-as.matrix(object@Cts.Mtx.bi)
               Cts.Mtx.bi<-Cts.Mtx.bi[,!colnames(Cts.Mtx.bi) %in% rmvariants]
               Cts.Mtx.bi<-Cts.Mtx.bi[rowSums(Cts.Mtx.bi)>0,]
@@ -1649,4 +1654,4 @@ Clonal_Variants<-c(Clonal_Variants,list(stat))
 }
 names(Clonal_Variants)<-unique(meta$Clone_merge)
 return(Clonal_Variants)
-}  
\ No newline at end of file
+}