From 734b5553f660e1dad8abc0cd151857d17d10f0c2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 20 Jun 2018 15:38:42 -0500
Subject: [PATCH] Fix R data file saves
---
r.scripts/sc-TissueMapper_RUN.D.R | 6 ++++++
r.scripts/sc-TissueMapper_RUN.D17.R | 8 +++++---
r.scripts/sc-TissueMapper_RUN.D27.R | 8 ++++++++
3 files changed, 19 insertions(+), 3 deletions(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.D.R b/r.scripts/sc-TissueMapper_RUN.D.R
index c060324..1606107 100644
--- a/r.scripts/sc-TissueMapper_RUN.D.R
+++ b/r.scripts/sc-TissueMapper_RUN.D.R
@@ -374,8 +374,14 @@ for (i in ls(pattern="^genes.deg")){
write.table(get(i),file=paste0("./analysis/deg/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
}
+save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
+rm(list=ls(pattern="sc10x.Stress"))
save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
rm(list=ls(pattern="^genes.deg"))
+save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
+rm(list=ls(pattern="^sc10x.Epi"))
+save(list=ls(pattern="sc10x.St"),file="./analysis/sc10x.St.Rda")
+rm(list=ls(pattern="sc10x.St"))
save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
rm(list=ls(pattern="^sc10x"))
save.image(file="./analysis/Data.RData")
diff --git a/r.scripts/sc-TissueMapper_RUN.D17.R b/r.scripts/sc-TissueMapper_RUN.D17.R
index d9240e1..9370de7 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17.R
+++ b/r.scripts/sc-TissueMapper_RUN.D17.R
@@ -390,12 +390,14 @@ rm(g)
scCustHeatmap(sc10x.Epi,i="Epi.dws.sub",gs=c(genes.deg.BE.unique,genes.deg.LE.unique,genes.deg.OE1.unique,genes.deg.OE2.unique),g=c("BE","LE","OE1","OE2"))
scCustHeatmap(sc10x.St,i="St.go",gs=c(genes.deg.Fib.unique,genes.deg.SM.unique,genes.deg.Endo.unique,genes.deg.OE2.unique,genes.deg.Leu.unique),g=c("Fib","SM","Endo","Leu"))
+save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
+rm(list=ls(pattern="sc10x.Stress"))
save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
rm(list=ls(pattern="^genes.deg"))
-save(list=ls(pattern="^sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
+save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
rm(list=ls(pattern="^sc10x.Epi"))
-save(list=ls(pattern="^sc10x.St"),file="./analysis/sc10x.St.Rda")
-rm(list=ls(pattern="^sc10x.St"))
+save(list=ls(pattern="sc10x.St"),file="./analysis/sc10x.St.Rda")
+rm(list=ls(pattern="sc10x.St"))
save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
rm(list=ls(pattern="^sc10x"))
save.image(file="./analysis/Data.RData")
diff --git a/r.scripts/sc-TissueMapper_RUN.D27.R b/r.scripts/sc-TissueMapper_RUN.D27.R
index 89fa46e..252034b 100644
--- a/r.scripts/sc-TissueMapper_RUN.D27.R
+++ b/r.scripts/sc-TissueMapper_RUN.D27.R
@@ -275,6 +275,14 @@ scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc")
scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc_NE")
scTables(sc10x,i.1="Merge_Epi.dws.sc_St.dws.sc_NE",i.2="Merge_Epi.dws.sc_St.dws.sc")
+save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
+rm(list=ls(pattern="sc10x.Stress"))
+save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
+rm(list=ls(pattern="^genes.deg"))
+save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
+rm(list=ls(pattern="^sc10x.Epi"))
+save(list=ls(pattern="sc10x.St"),file="./analysis/sc10x.St.Rda")
+rm(list=ls(pattern="sc10x.St"))
save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
rm(list=ls(pattern="^sc10x"))
save.image(file="./analysis/Data.RData")
--
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