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kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq
https://kharchenkolab.github.io/numbat/
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Refining tumor/normal assignment #209

Open nandobonf opened 3 weeks ago

nandobonf commented 3 weeks ago

Dear authors, I successfully ran Numbat on multiple samples, however in some cases I would need to refine the tumor/normal definition (or eventually remove "noisy" CNV calls such as the BAMP). In the case shown below, for example, it is clear that genotypes 1 and 2 demote normal cells, instead, Numbat only calls genotype 1 as "normal". You can see the Numbat tumor/normal annotation labeled as "type" in the heatmap below. Any suggestions would be highly appreciated. Thanks in advance.

image
teng-gao commented 3 days ago

Hi,

In this case you can add up probabilities of clone_1 and clone_2 (fromclone_post) and use that as normal probability. This works because clone_post contains clonal assignment probabilities, and for each cell they sum to one.

Best, Teng