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jlaffy / infercna

Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
http://jlaffy.github.io/infercna
GNU General Public License v3.0
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Some questions about infercna #1

Open YiweiNiu opened 5 years ago

YiweiNiu commented 5 years ago

Dear Laffy,

I read your new glioblastoma paper and would like to try your methods on our single-cell RNA-seq data.

But I have the following concerns.

  1. What is the differences between this package and infercnv? Intuitively, I found infercnv is much more complicated.

  2. When using infercna(), can I pool all samples (different tumors) together? Or it should be applied to individual sample? Since Figure 1A in your paper show all samples in one heatmap, I guess you put all cells in one matrix, is that true? I do not know if pooling different tumors is a good way, as inter-tumor heterogeneity may influence the results.

  3. Did you use refCells in analyzing the glioblastoma data? Or you classify malignant cells and non-malignant cells by combining CNA signal and CNA correlation? In the method "CNA inference from single-cell data", it said cells were classified by CNA signal and CNA correlation, but the upper panel in Figure 1A shows the CNA levels of non-malignant cells. So, I am confused.

It would be highly appreciated if you could give me some hints. I am new to single-cell data analysis.

Best wishes, Yiwei Niu

twoneu commented 1 year ago

Hi @jlaffy,

I am also curious about @YiweiNiu's questions 1 and 2. Do we expect the results to be comparable between this package and inferCNV?

Also, what do you recommend for a sample containing few/no normal reference cells?