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GfellerLab / EPIC

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
https://gfellerlab.shinyapps.io/EPIC_1-1/
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Custom Signature genes #7

Closed Disha770 closed 3 years ago

Disha770 commented 4 years ago

Hi, I was wondering if I can provide a custom signature gene file in epic? If yes then can you tell me how can I do that ? Thank you in advance.

jracle85 commented 4 years ago

Hi Disha,

Yes, you can define your own gene expression reference profiles and genes signatures to use with them.

This corresponds to the input option called reference. You can check the help page of EPIC for details (browse to it with e.g. ?EPIC::EPIC from within R). And you can see examples of such references in EPIC::TRef for example.

Best wishes,

Julien

Disha770 commented 4 years ago

Hi, Thank you for your suggestion but can I add my own signature genes to the TRef?

jracle85 commented 4 years ago

Hello, If you want to use your own gene signature to use with the reference profiles TRef, you can use the option sigGenes from EPIC, with a character vector giving the gene names to use as signature (it replaces the ones used by default for TRef, it doesn't add them - to add them, just add the ones given in EPIC::TRef$sigGenes to your list). Best regards, Julien