Make QuSAGE for Lineage and Epi use DWS 5FC DEGs

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)

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)