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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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How scCancer handle the hg19 and hg38 for the interaction score? #8

Closed Puriney closed 4 years ago

Puriney commented 4 years ago

https://github.com/wguo-research/scCancer/blob/3f9eb9e878531d588594a132f00d60d6d38506c8/R/scAnnotation.R#L1297

It seems FANTOM database has hg38 and hg19 annotations. I was wondering how scCancer, in particular, scAnnotate, handles this? For example, if my scRNA-seq data is mapped to hg38 whereas the default of scCancer is hg19, how would scCancer knows this and properly run cell interaction?

wguo-research commented 4 years ago

I only used the ligand-receptor pair data of FNATOM database. It seems to only have gene names, without hg38 and hg19 annotations.