Regarding copykat, it defines aneuploidy for the specified normal group
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 42/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Quiet
- Tech stack
- r
- Domain
- bioinformatics
Research direction
Start at the copykat() entry point and review how the norm.cell.names argument is documented and used with the supplied R code. Reproduce the run with the Hep_5 subgroup and inspect whether the reported aneuploidy is expected; the issue is resolved when the behavior or a code problem is clearly identified.
Written by the indexing model from the issue text.
Description
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
- Dominant language
- R
- Stars
- 305
- Forks
- 66
- PR merge metrics
- No merged PRs in 30d
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