Skip to content

Regarding copykat, it defines aneuploidy for the specified normal group #129

@mosy550

Description

@mosy550

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

Image

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions