Commit 1337e208 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Fix QC filtering

parent c07f465f
......@@ -160,14 +160,13 @@ scQC <- function(sc10x,sub=FALSE,sp="hu"){
threshPlot <- list()
cell.remove <- NULL
Idents(object=sc10x) <- "samples"
sc10x.sub <- sc10x
for (i in c("nFeature_RNA","percent.mito")){
if (i %in% c("nCount_RNA","nFeature_RNA")){
thresh <- scThresh(sc10x.sub,feature=i,direction="b",name=i)
thresh <- scThresh(sc10x,feature=i,direction="b",name=i)
} else {
thresh <- scThresh(sc10x.sub,feature=i,direction="h",name=i)
thresh <- scThresh(sc10x,feature=i,direction="h",name=i)
}
data <- FetchData(sc10x.sub,vars=i)
data <- FetchData(sc10x,vars=i)
if (i %in% c("nCount_RNA","nFeature_RNA")){
cell.remove <- c(cell.remove,rownames(data)[data[,1] < thresh[[2]] | data[,1] > thresh[[1]]])
} else {
......@@ -177,6 +176,7 @@ scQC <- function(sc10x,sub=FALSE,sp="hu"){
plot(thresh[[3]])
dev.off()
}
sc10x.sub <- subset(sc10x,cells=WhichCells(sc10x,cells=cell.remove,invert=TRUE))
# threshPlot <- list()
# cell.remove <- NULL
......
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