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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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GSVA error #62

Closed tonyjhlam closed 2 years ago

tonyjhlam commented 2 years ago

Getting the following error when running run_gsva()

run_gsva(as.data.frame(expression), network = dre, method='gsva')

unable to find an inherited method for function ‘gsva’ for signature ‘"data.frame", "list"’

PauBadiaM commented 2 years ago

Hi @tonyjhlam,

Thanks for checking out the package! Unfortunately decoupleR only accepts matrices as input mat, not data-frames. Whenever I have time I'll write a function that checks for this. Try it with a named matrix (with gene and sample or contrast names) and let me know please. Hope this was helpful.

tonyjhlam commented 2 years ago

Thanks @PauBadiaM this seems to have solved the issue.