From b6ebab19dc6e41663b60848219cd3917c4c7e8f9 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 14 Jul 2018 23:17:10 -0500
Subject: [PATCH] Filter DEGs to only be a adj-p-value <=0.05, and loosen DEG
criteria for NEs to genes present in 1% of cells and min of 1FC
---
r.scripts/sc-TissueMapper.R | 1 +
r.scripts/sc-TissueMapper_RUN.D17.R | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R
index 0c1d52f..702ab55 100644
--- a/r.scripts/sc-TissueMapper.R
+++ b/r.scripts/sc-TissueMapper.R
@@ -972,6 +972,7 @@ scTables <- function(sc10x,i.1,i.2){
scDEG <- function(sc10x,i="Lin",g.1="Epi",g.2="St",pct=0.25,t=2){
sc10x <- SetAllIdent(object=sc10x,id=i)
genes.deg <- FindMarkers(object=sc10x,ident.1=g.1,ident.2=g.2,min.pct=pct,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(t))
+ genes.deg <- genes.deg[genes.deg$p_val_adj<=0.05,]
return(genes.deg)
}
diff --git a/r.scripts/sc-TissueMapper_RUN.D17.R b/r.scripts/sc-TissueMapper_RUN.D17.R
index da6ef49..1b639cf 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17.R
+++ b/r.scripts/sc-TissueMapper_RUN.D17.R
@@ -280,7 +280,7 @@ genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","LE","OE1
genes.deg.OE1 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE1",g.2=c("BE","LE","OE2"),pct=0.25,t=2)
genes.deg.OE2 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE2",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
-genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2="ALL",pct=0.25,t=2)
+genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2="ALL",pct=0.01,t=1)
genes.deg.Fib <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="Fib",g.2=c("SM","Endo","Leu"),pct=0.25,t=2)
genes.deg.SM <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="SM",g.2=c("Fib","Endo","Leu"),pct=0.25,t=2)
--
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