Thank you for developing such a useful package. I am applying infercnv to 10X scRNA-seq data to infer gene copy number for each single cell. I am wondering if I can use the data in count.data slot to roughly estimate the actual copy number of genes of interests for each cell? In my case, the reference group are cells with low gene copy numbers, and the malignant cell group are cells with high gene copy numbers. If I calculate the ratio between low and high gene copy number cells using the data from count.data slot, can it roughly give me the information of how much copy number is multiplied between reference cells and malignant cells? Also, could you explain the meaning of count.data slot of an infercnv object and what I can use it for?
Dear infercnv development/maintenance group,
Thank you for developing such a useful package. I am applying infercnv to 10X scRNA-seq data to infer gene copy number for each single cell. I am wondering if I can use the data in count.data slot to roughly estimate the actual copy number of genes of interests for each cell? In my case, the reference group are cells with low gene copy numbers, and the malignant cell group are cells with high gene copy numbers. If I calculate the ratio between low and high gene copy number cells using the data from count.data slot, can it roughly give me the information of how much copy number is multiplied between reference cells and malignant cells? Also, could you explain the meaning of count.data slot of an infercnv object and what I can use it for?
Thank you very much in advance!
Yue