Hello.
When I was running copykat, I specified a subgroup as normal cells. But why did the result of running it also define aneuploidy within this subgroup? Part of my code is as follows:
normal_cells <- rownames(msy@meta.data)[
msy@meta.data$Hep_res_0.3 == "Hep_5"
]
exp.rawdata <- as.matrix(msy@assays$RNA@counts)
copykat.test <- copykat(rawmat=exp.rawdata,
id.type="S",
ngene.chr=5,
win.size=25,
KS. The cut = 0.1,
sam.name="test",
distance="spearman",
norm.cell.names=normal_cells,
output.seg="FALSE",
plot.genes="TRUE",
genome="mm10",
n.cores=8)
May I ask if there is a problem with my code?
Thank you very much
