From 68fdeb80fa11176b2a00296a7d98d070eb9ebca6 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 9 Oct 2018 16:55:41 -0500
Subject: [PATCH] Fix min st cluster size for QuSAGE
---
r.scripts/sc-TissueMapper_RUN.Pd.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index 2b76a12..7772609 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -312,7 +312,7 @@ names(gene.set1) <- "Leu"
gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
-min.st <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
+min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=0.2,ds=min.st,nm="St.go",folder="st")
sc10x.St <- results[[1]]
results.cor.St.go <- results[[2]]
--
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