class "filtered" of cells

[Ilarius]

Hello,
when looking at my results I found that a consistent set of cells receive a "filtered" label instead of normal/tumor.
Why is that?
In the paper it says that cells with less than 200 genes get filtered out but I already excluded cells with less than 500 genes.
However I do see that these cells have worse statistics.
What are the criteria to filter these cells out?

summary(seu$nFeature_RNA[which(seu$SCEVAN=="filtered")])
Min. 1st Qu. Median Mean 3rd Qu. Max.
500.0 552.0 627.0 697.3 758.0 3933.0
summary(seu$nCount_RNA[which(seu$SCEVAN=="filtered")])
Min. 1st Qu. Median Mean 3rd Qu. Max.
556.0 715.0 838.0 990.2 1075.0 10535.0

[AntonioDeFalco]

Hello @Ilarius,
As you can see in the public code during the pre-processing phase (code), in addition to cells filtered by gene number, other cells are filtered out if they do not have at least 5 genes expressed on each chromosome (a necessary QC condition for copy number analysis).

Regards.