Commit 127fdb34 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Replace sc_QC parameters as seurat subset has error reading variables inside functions

parent 908e1bbc
......@@ -26,13 +26,19 @@ scFolders()
sc10x <- scLoad(p=project.name)
results <- scQC(sc10x,lg=500,hg=2500,hm=0.1,sub=FALSE)
lg=500
hg=2500
hm=0.1
results <- scQC(sc10x,lg=lg,hg=hg,hm=hm,sub=FALSE)
sc10x <- results[[1]]
counts.cell.raw <- results[[2]]
counts.gene.raw <- results[[3]]
counts.cell.filtered <- results[[4]]
counts.gene.filtered <- results[[5]]
rm(results)
rm(lg)
rm(hg)
rm(hm)
results <- scCellCycle(sc10x,sub=FALSE)
sc10x <- results[[1]]
......
......@@ -146,9 +146,9 @@ scQC <- function(sc10x,lg=500,hg=2500,hm=0.1,sub=FALSE){
counts.gene.raw <- nrow(GetAssayData(object=sc10x,slot="counts"))
#Filter/normalize data
sc10x.sub <- subset(x=sc10x,subset=nFeature_RNA > lg)
sc10x.sub <- subset(x=sc10x.sub,subset=nFeature_RNA < hg)
sc10x.sub <- subset(x=sc10x.sub,subset=percent.mito < hm)
sc10x.sub <- subset(x=sc10x,subset= nFeature_RNA > lg)
sc10x.sub <- subset(x=sc10x.sub,subset= nFeature_RNA < hg)
sc10x.sub <- subset(x=sc10x.sub,subset= percent.mito < hm)
sc10x.sub <- NormalizeData(object=sc10x.sub,normalization.method="LogNormalize",scale.factor=10000,verbose=FALSE)
#Plot filtered stats
......
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