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Commit 9f68003a authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Fix Lin QuSAGE and rm commands

parent b02878f8
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......@@ -91,7 +91,7 @@ option_list=list(
make_option("--hpc",action="store",default=0.7,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
make_option("--stg",action="store",default="go",type='character',help="Geneset to use for stress ID"),
make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
make_option("--hpc.poststress",action="store",default=0.7,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
make_option("--ds",action="store",default=0,type='integer',help="Number of cells to downsample"),
......@@ -151,12 +151,12 @@ if (opt$st==TRUE){
sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=opt$res.poststress,folder="post.stress")
}
gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
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 <- as.list(gene.set1)
names(gene.set1) <- "St"
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 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
gene.set1 <- gene.set1[1]
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
......@@ -342,7 +342,7 @@ for (i in ls(pattern="^genes.deg")){
}
save(list=ls(pattern="^genes.deg"),file="./analysis/DEG.Rda")
rm(ls(pattern="^genes.deg"))
rm(list=ls(pattern="^genes.deg"))
save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
rm(ls(pattern="^sc10x"))
rm(list=ls(pattern="^sc10x"))
save.image(file="./analysis/Data.RData")
\ No newline at end of file
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