From e42b9eea91ed65c864a2711c191ac430f5a9c81e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 4 Nov 2018 23:48:51 -0600
Subject: [PATCH] Don't downsample FACS analysis
---
r.scripts/sc-TissueMapper_RUN.D17_FACS.R | 6 +++---
r.scripts/sc-TissueMapper_RUN.D27_FACS.R | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
index 7812cd1..d884b5f 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
+++ b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
@@ -180,7 +180,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.all <- min(table(sc10x@meta.data[,paste0("res",opt$res.poststress)]))
-results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder="lin")
+results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Lin",folder="lin")
sc10x <- results[[1]]
results.cor.Lin <- results[[2]]
results.clust.Lin.id <- results[[3]]
@@ -254,7 +254,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.epi <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
-results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=min.epi,nm="Epi.dws.sc",folder="epi")
+results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Epi.dws.sc",folder="epi")
sc10x.Epi <- results[[1]]
results.cor.Epi.dws <- results[[2]]
results.clust.Epi.dws.id <- results[[3]]
@@ -284,7 +284,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
-results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=min.st,nm="St.dws.sc",folder="st")
+results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="St.dws.sc",folder="st")
sc10x.St <- results[[1]]
results.cor.St.go <- results[[2]]
results.clust.St.go.id <- results[[3]]
diff --git a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
index 61cadc9..a7328b8 100644
--- a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
+++ b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
@@ -180,7 +180,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.all <- min(table(sc10x@meta.data[,paste0("res",opt$res.poststress)]))
-results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder="lin")
+results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Lin",folder="lin")
sc10x <- results[[1]]
results.cor.Lin <- results[[2]]
results.clust.Lin.id <- results[[3]]
@@ -254,7 +254,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.epi <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
-results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=min.epi,nm="Epi.dws.sc",folder="epi")
+results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="Epi.dws.sc",folder="epi")
sc10x.Epi <- results[[1]]
results.cor.Epi.dws <- results[[2]]
results.clust.Epi.dws.id <- results[[3]]
@@ -284,7 +284,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
-results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=min.st,nm="St.dws.sc",folder="st")
+results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=0,nm="St.dws.sc",folder="st")
sc10x.St <- results[[1]]
results.cor.St.go <- results[[2]]
results.clust.St.go.id <- results[[3]]
--
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