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Commit 58946a86 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix D27 and D

parent eb9a35b0
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...@@ -202,9 +202,9 @@ if (any(levels(sc10x@ident)=="Unknown")){ ...@@ -202,9 +202,9 @@ if (any(levels(sc10x@ident)=="Unknown")){
#pc.use.epi <- results[[3]] #pc.use.epi <- results[[3]]
#rm(results) #rm(results)
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=0.1,folder="epi") sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=0.5,folder="epi") sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=opt$res.epi,folder="epi") sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE) gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- gene.set1[1] gene.set1 <- gene.set1[1]
......
...@@ -182,9 +182,9 @@ if (any(levels(sc10x@ident)=="Unknown")){ ...@@ -182,9 +182,9 @@ if (any(levels(sc10x@ident)=="Unknown")){
#pc.use.epi <- results[[3]] #pc.use.epi <- results[[3]]
#rm(results) #rm(results)
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=0.1,folder="epi") sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=0.5,folder="epi") sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.epi,res.use=opt$res.epi,folder="epi") sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE) gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- gene.set1[1] gene.set1 <- gene.set1[1]
...@@ -220,9 +220,9 @@ rm(gene.set) ...@@ -220,9 +220,9 @@ rm(gene.set)
#pc.use.st <- results[[3]] #pc.use.st <- results[[3]]
#rm(results) #rm(results)
sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.st,res.use=0.1,folder="st") sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.1,folder="st")
sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.st,res.use=0.5,folder="st") sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=0.5,folder="st")
sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.st,res.use=opt$res.st,folder="st") sc10x.St <- scCluster(sc10x.St,pc.use=pc.use.poststress,res.use=opt$res.st,folder="st")
gene.set1 <- read_delim("./genesets/genes.deg.Fib.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE) gene.set1 <- read_delim("./genesets/genes.deg.Fib.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- gene.set1[1] gene.set1 <- gene.set1[1]
......
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