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Commit e42b9eea authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Don't downsample FACS analysis

parent 988b20ad
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1 merge request!6Develop
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r.scripts/sc-TissueMapper_RUN.D17_FACS.R
+ 3
− 3
View file @ e42b9eea
......@@ -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$res.poststress,ds=0,nm="St.dws.sc",folder="st")
sc10x.St <- results[[1]]
results.cor.St.go <- results[[2]]
results.clust.St.go.id <- results[[3]]
......
r.scripts/sc-TissueMapper_RUN.D27_FACS.R
+ 3
− 3
View file @ e42b9eea
......@@ -180,7 +180,7 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
min.all <- min(table(sc10x@meta.data[,paste0("res",opt$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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