Estimation of Copy Number of alterations(CNA) in Sc-RNA Seq data

Question

[Maria17]

Hi All,

I'm working on single-cell RNA seq data mostly with the Seurat package and SCE object. I need to estimate Copy number alterations/aberrations (CNAs) for my data but I could not find that many tools for this purpose.

Any recommendation tools in R (preferably applicable of Seurat object or Sce object) for the estimation of CNAs would be appreciated. Thanks. Maria

Answer 1

[jared.andrews07]

There are several tools for this. inferCNV and CONICSmat are two that are fairly easy to use and that I've seen cited a few times. It's easy to run both from SCE or Seurat objects.

[Maria17]

@jared.andrews07, Thank you, I was trying to use inferCNV on my Seurat object. but inferCNV requires 4 different files which I was not able to implement. I just could extract the count file from my Seurat object. I annotated my raw data and have symbols and gene names and chromosome positions in my Seurat object. also, I annotated cell types with SingleR library and have a cell types column in my object.

[jared.andrews07]

Okay, well, all of those inputs are pretty straightforward, so I'm not sure what exactly you're having issues with without you telling us.

Answer 2

[igor]

I could not find that many tools for this purpose

This previous discussion has a few: Detecting copy number alterations based on RNA-seq data