I understand that the primary purpose of infercnv is not to separate within epithelial cells into normal & tumour cells, however I would need this kind of separation for a current project.
I have been running inferCNV with a reference (all other cells apart from epithelial cells) and obtained the below heatmap:
As mentioned I would like to separate now my normal and tumour epithelial cells:
I was able to access the 28 subclusters of epithelial cells via
I guess I can visually more or less separate them (assuming subcluster epithelial 10 is the the yellow within the epithelial cells, then cluster 1, 3.. ) however I would prefer a "safer" approach. Could you advice me how to do so?
I read this post (https://www.biostars.org/p/9573777/) about calculating a score, however I am not sure how to perform this for only epithelial cells.
Good afternoon,
I understand that the primary purpose of infercnv is not to separate within epithelial cells into normal & tumour cells, however I would need this kind of separation for a current project. I have been running inferCNV with a reference (all other cells apart from epithelial cells) and obtained the below heatmap:
As mentioned I would like to separate now my normal and tumour epithelial cells: I was able to access the 28 subclusters of epithelial cells via
infercnv_obj@tumor_subclusters$subclusters$Epithelial cells``I guess I can visually more or less separate them (assuming subcluster epithelial 10 is the the yellow within the epithelial cells, then cluster 1, 3.. ) however I would prefer a "safer" approach. Could you advice me how to do so?
I read this post (https://www.biostars.org/p/9573777/) about calculating a score, however I am not sure how to perform this for only epithelial cells.
Thank you for any advice!