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DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
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GeneSet issue with singscore #18

Closed NMaziak closed 4 years ago

NMaziak commented 4 years ago

Hello,

I was wondering if you could provide how the tgfb genesets were derived. These sets work, but when I have made ones I'm having a hard time making my gene list (which is just the gene symbols e.g. KRT19, AGR2...) to be properly set up with the same geneIds method as you have used. I'm sorry, I'm very new to this and have been stuck on how to move forward.

Cheers, Noura

bhuvad commented 4 years ago

Hi Noura,

Thanks for using singscore. Singscore accepts simple character vectors (e.g. sig<- c('KRT19', 'AGR2')) so you do not necessarily need to create a GeneSet object (which is what we usually create). If you are keen to create a GeneSet object, you can do so as shown below:

library(GSEABase)

sig_genes <- c('KRT19', 'AGR2') #you can use this directly in simpleScore
sig <- GeneSet(sig_genes, setName = 'MySet')