search

DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
40 stars 5 forks source link

Unable to create a gene set #35

Closed Bioinformatika-BWID closed 2 years ago

Bioinformatika-BWID commented 2 years ago

Hi, Can you kindly show me the code you used to create tgfb_gs_up? I am trying to create a geneset object for analysis in singscore and it is proving impossible because it is not clear what line of code you used.

I used this line of code and got the following error.

Kind regards

image

image

ruqianl commented 2 years ago

Hi @bioinformaticulus ,

Thanks for trying our tool.

A short example of creating a GeneSet object:

BiocManager::install("GSEABase")
BiocManager::install("GO.db")
library(GSEABase)
GeneSet(geneIds = c("geneName1","geneName2"), geneIdType=SymbolIdentifier())

To view more details of the GeneSet class

?GSEABase::GeneSet

And the error you had regarding GO would be resolved by installing the GO.db package BiocManager::install("GO.db")

Ruqian

Bioinformatika-BWID commented 2 years ago

Thank you very much, I will try that now.