From 2d5d563b275b6fbff040faa115eeeb9a633382f3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 30 Apr 2018 15:07:57 -0500
Subject: [PATCH] Make QuSAGE for Lineage and Epi use DWS 5FC DEGs
---
r.scripts/sc_QuSAGE.Lineage.R | 4 ++--
r.scripts/sc_QuSAGE_EpiSubClust.R | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/r.scripts/sc_QuSAGE.Lineage.R b/r.scripts/sc_QuSAGE.Lineage.R
index 076e212..faeba90 100755
--- a/r.scripts/sc_QuSAGE.Lineage.R
+++ b/r.scripts/sc_QuSAGE.Lineage.R
@@ -73,11 +73,11 @@ for (i in 1:Number.Clusters){
cC[i] <- paste0("Cluster_",i,"-REST")
}
rm(labels)
-gene.set2 <- read_delim("./genesets/DEG_FMSt_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "St"
gene.set <- c(gene.set2)
-gene.set2 <- read_delim("./genesets/DEG_Epi_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "Epi"
gene.set <- c(gene.set,gene.set2)
diff --git a/r.scripts/sc_QuSAGE_EpiSubClust.R b/r.scripts/sc_QuSAGE_EpiSubClust.R
index be4edef..dbfcc06 100755
--- a/r.scripts/sc_QuSAGE_EpiSubClust.R
+++ b/r.scripts/sc_QuSAGE_EpiSubClust.R
@@ -90,15 +90,15 @@ if (opt$lgea==TRUE){
sets=c(sets,"lgea")
}
-gene.set2 <- read_delim("./genesets/DEG_BE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "BE"
gene.set <- c(gene.set2)
-gene.set2 <- read_delim("./genesets/DEG_LE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_LE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "LE"
gene.set <- c(gene.set,gene.set2)
-gene.set2 <- read_delim("./genesets/DEG_OE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_OE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "OE"
gene.set.dws <- c(gene.set,gene.set2)
--
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