From c07187017171d1437d9815216e12dd74d09f854e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 3 Nov 2018 13:18:51 -0500
Subject: [PATCH] Increase stringency for pan Epi and St DEG calc to 75% of
pops and 2FC
---
r.scripts/sc-TissueMapper_RUN.Pd.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index cda01c1..c68ab80 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -409,8 +409,8 @@ scTables(sc10x,i.1="Merge_Epi.dws_St.go_NE",i.2="Merge_Epi.dws_St.go")
genes.deg.Stress <- scDEG(sc10x.Stress,i="Stress",g.1="Stress",g.2="ALL",pct=0.5,t=5)
-genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=2)
-genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=2)
+genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",pct=0.75,t=2)
+genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",pct=0.75,t=2)
genes.deg.BE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="BE",g.2=c("LE","OE1","OE2"),pct=0.25,t=2)
genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","OE1","OE2"),pct=0.25,t=2)
--
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