From 1debf5707edded58e3351e8ca71094579f99e4fb Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 17 Dec 2018 12:06:40 -0600
Subject: [PATCH] Fix run_Pd for Hillock geneset
---
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 81cbf9a..396cf44 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -377,7 +377,7 @@ gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "Ionocyte"
gene.set <- c(gene.set,gene.set2)
rm(gene.set2)
-gene.set1 <- read_csv("./genesets/SupTab6_Krt13_Hillock.csv",skip=5)
+gene.set1 <- read_csv("./genesets/SupTab6_Krt13_Hillock.csv")
gene.set1 <- gene.set1[gene.set1$FDR<=0.05 & gene.set1$'log2 fold-change (MAST)'>=1.5,1]
colnames(gene.set1) <- "genes"
gene.set1 <- as.data.frame(merge(gene.set1,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
--
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