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BaderLab / Tempora

Pathway-based trajectory inference method for time-series scRNAseq data
MIT License
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CalculatePWProfiles issue - invalid class "GeneSetCollection" object #14

Open sciotlos opened 3 years ago

sciotlos commented 3 years ago

Hello again,

After correcting the CreateSeuratObject issue, I've run into the following issue when calling CalculatePWPProfiles as:

CalculatePWProfiles(temporaObj, gmt_path ="Human_GOBP_AllPathways_no_GO_iea_January_13_2021_symbol.gmt",
                                        method="gssea", min.sz = 5, max.sz = 200, parallel.sz = 1)

and here is the error:

Calculating cluster average gene expression profile...Error in validObject(.Object) : 
  invalid class "GeneSetCollection" object: superclass "vector_OR_Vector" not defined in the environment of the object's class

I have tried a few things, reinstalling packages, checking my data's structure, etc.. no luck.. any ideas? Thanks again! -Serban

risserlin commented 3 years ago

I don't think this is the issue because when I run your code I get a different error.
The method should be "ssgsea" not "gssea"

Is your data a seurat object or is it an expression matrix?