From 4115d3bc038cdbfacaa56da13f2362ad86289a9e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 15 Aug 2018 22:59:54 -0500
Subject: [PATCH] Change res for St to 0.3 and change cutoff for NE to 0.1% in
D17
---
r.scripts/sc-TissueMapper_RUN.D17.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.D17.R b/r.scripts/sc-TissueMapper_RUN.D17.R
index e085e95..3f2594a 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17.R
+++ b/r.scripts/sc-TissueMapper_RUN.D17.R
@@ -102,7 +102,7 @@ option_list=list(
#make_option("--hpc.epi",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
make_option("--res.epi",action="store",default=0.2,type='numeric',help="Resolution to cluster, Epi"),
#make_option("--hpc.st",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, St"),
- make_option("--res.st",action="store",default=0.2,type='numeric',help="Resolution to cluster, St")
+ make_option("--res.st",action="store",default=0.3,type='numeric',help="Resolution to cluster, St")
)
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
@@ -250,7 +250,7 @@ results.clust.St.go.id <- results[[3]]
rm(results)
rm(gene.set)
-sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=0.95)
+sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=0.999)
sc10x.Epi <- scMergeSubClust(sc10x.Epi,i="Epi.dws.sub",g=c("BE","LE"),nm="Merge")
--
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