Fix sc_Demultiplex.R from previous commit and fix QuSAGE Epi+St SubClust

r.scripts/sc_Demultiplex.R

@@ -6,7 +6,7 @@ library(readr)
 
 #retrive command line options
 option_list=list(
-  make_option("--p",action="store",default="ALL",type='character',help="Project Name"),
+  make_option("--p",action="store",default="Pr",type='character',help="Project Name"),
   make_option("--d",action="store",default=4,type='integer',help="Demultiplex Group Number"),
   make_option("--mc",action="store",default=3,type='integer',help="Minimum Cells"),
   make_option("--mg",action="store",default=200,type='integer',help="Minimum Genes")

r.scripts/sc_QuSAGE_EpiSubClust.R

@@ -287,7 +287,7 @@ rm(Number.Clusters)
 opt.episubclust <- opt
 rm(opt)
 
-#save QuSAGE.EpiPop.Rda,IDepi.Rda file,Cumulative.RData files
+#save QuSAGE.Epi.Rda,IDepi.Rda file,Cumulative.RData files
 save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.episubclust$g,sub.file,".QuSAGE.Epi.Rda"))
 rm(list=ls(pattern="^qs."))
 save(sc10x.Group,file=paste0("./analysis/sc10x.",Project.Name,".",opt.episubclust$g,".cluster",sub.file,".IDepi.Rda"))

r.scripts/sc_QuSAGE_StSubClust.R

@@ -13,7 +13,7 @@ option_list=list(
   make_option("--r",action="store",default=0.1,type='numeric',help="Resolution"),
   make_option("--st",action="store",default=TRUE,type='logical',help="Analyze Data With Stress Pops Removed?"),
   make_option("--s",action="store",default=5000,type='integer',help="Number Of Cells To Downsample To"),
-  make_option("--lgea",action="store",default=TRUE,type='logical',help="Correlate to LGEA Epi?"),
+  make_option("--lgea",action="store",default=TRUE,type='logical',help="Correlate to LGEA St?"),
   make_option("--c2",action="store",default=FALSE,type='logical',help="Correlate to c2?"),
   make_option("--c5",action="store",default=FALSE,type='logical',help="Correlate to c5?")
 )
@@ -253,12 +253,12 @@ rm(Number.Clusters)
 opt.stsubclust <- opt
 rm(opt)
 
-#save QuSAGE.EpiPop.Rda,IDepi.Rda file,Cumulative.RData files
-save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.episubclust$g,sub.file,".QuSAGE.Epi.Rda"))
+#save QuSAGE.St.Rda,IDepi+st.Rda file,Cumulative.RData files
+save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.stsubclust$g,sub.file,".QuSAGE.St.Rda"))
 rm(list=ls(pattern="^qs."))
-save(sc10x.Group,file=paste0("./analysis/sc10x.",Project.Name,".",opt.episubclust$g,".cluster",sub.file,".IDepi.Rda"))
+save(sc10x.Group,file=paste0("./analysis/sc10x.",Project.Name,".",opt.stsubclust$g,".cluster",sub.file,".IDepi+st.Rda"))
 rm(sc10x.Group)
-save(sc10x.Group.St,file=paste0("./analysis/sc10x.",Project.Name,".",opt.stsubclust$g,".StSubcluster",sub.file,".IDepi.Rda"))
+save(sc10x.Group.St,file=paste0("./analysis/sc10x.",Project.Name,".",opt.stsubclust$g,".StSubcluster",sub.file,".IDst.Rda"))
 rm(sc10x.Group.St)
 rm(sub.folder)
 rm(sub.file)