ssGSEA Error About GSVA

ncborcherding / escape

Easy single cell analysis platform for enrichment

https://www.borch.dev/uploads/screpertoire/articles/running_escape

MIT License

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ssGSEA Error About GSVA #88

Closed DarioS closed 8 months ago

DarioS commented 8 months ago

I updated to the development version. The default settings fail due to some function call to GSVA.

> runEscape(fibroblasts, hallmarkSet)
[1] "Using sets of 1000 cells. Running 35 times."
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘gsva’ for signature ‘"missing", "missing"’

ncborcherding commented 8 months ago

Hey Dario,

This is a GSVA version issue that will be resolved with the next bioconductor release.

For now, you can install GSVA from the repo using:

devtools::install_github("rcastelo/GSVA")

Nick