From ca6ba2ef3be400b46db9426d1093bdec2899c39f Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 10 Nov 2018 11:04:24 -0600
Subject: [PATCH] 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 | 7 +++----
r.scripts/sc-TissueMapper_RUN.D27_FACS.R | 7 +++----
r.scripts/sc-TissueMapper_RUN.DS_D17.R | 6 ++----
3 files changed, 8 insertions(+), 12 deletions(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
index 7812cd1..fb8f5a8 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
+++ b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
@@ -167,13 +167,12 @@ if (opt$st==TRUE){
sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
}
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "St"
gene.set <- c(gene.set,gene.set1)
diff --git a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
index 61cadc9..0337bd6 100644
--- a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
+++ b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
@@ -167,13 +167,12 @@ if (opt$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)
diff --git a/r.scripts/sc-TissueMapper_RUN.DS_D17.R b/r.scripts/sc-TissueMapper_RUN.DS_D17.R
index fb7d2bc..efec340 100644
--- a/r.scripts/sc-TissueMapper_RUN.DS_D17.R
+++ b/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)
--
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