Revert all analysis to use dws bulk pan Epi and St genelists for lin ID with QuSAGE

r.scripts/sc-TissueMapper_RUN.D17_FACS.R

@@ -167,13 +167,12 @@ if (opt$st==TRUE){
   sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
 }
 
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
 names(gene.set1) <- "Epi"
 gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
 names(gene.set1) <- "St"
 gene.set <- c(gene.set,gene.set1)

r.scripts/sc-TissueMapper_RUN.D27_FACS.R

@@ -167,13 +167,12 @@ if (opt$st==TRUE){
   sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
 }
 
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
 names(gene.set1) <- "Epi"
 gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
 names(gene.set1) <- "St"
 gene.set <- c(gene.set,gene.set1)

r.scripts/sc-TissueMapper_RUN.DS_D17.R

@@ -180,13 +180,11 @@ if (opt$st==TRUE){
   sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=opt$res.poststress,folder="post.stress",red="pca")
 }
 
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
 names(gene.set1) <- "Epi"
 gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set1 <- as.list(gene.set1)
 names(gene.set1) <- "St"
 gene.set <- c(gene.set,gene.set1)