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dviraran / xCell

Cell types enrichment analysis
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export gene X cell #50

Open abehd1 opened 3 years ago

abehd1 commented 3 years ago

Hello there!

Thank you for this awesome R package. I have a question regarding exporting files. I have run xCell on bulk RNA seq data. The usual result gives me a matrix of enriched cell types across samples. However, I want a matrix of enriched cell type across the genes that were used in the process. Is there a way to export the enrichment score across the used genes and not samples?

Thanks again.

dviraran commented 3 years ago

Thanks!

I am not sure I understand - what is enriched cell types across genes? If you are looking for the reference signatures you can find them in xCell.data$signatures.

Best, Dvir

abehd1 commented 3 years ago

Thank you for the prompt response! Can I just use the unique gene identifiers in the reference signature as 'markers' for the cell types?

dviraran commented 3 years ago

Yes, those are not perfect markers, but as a group they are supposed to be markers.