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saezlab / dorothea

R package to access DoRothEA's regulons
https://saezlab.github.io/dorothea/
GNU General Public License v3.0
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df2regulon function returns list instead of regulon object #32

Closed justinjacobse closed 3 years ago

justinjacobse commented 3 years ago

Dear developers,

I'm trying to run msVIPER on a DESeq2 dataset. With converting the dorothea regulons to a format suitable for msVIPER, I run into the problem that the output of the code below (thanks Christian for pointing me to this function) is a list, and not a regulon object. Could you please help me further?

# Load dorothea
library("dorothea")
# Load mm data from dorothea
data(dorothea_mm, package ="dorothea")
# Convert to the format required by viper
viper_regulons <- dorothea::df2regulon(dorothea_mm)

Thanks, Justin

christianholland commented 3 years ago

Hi Justin,

EDIT: Please apologise now I understand your issue.

Indeed, the function df2regulon returns a list. I am aware of that the documentation of msviper requires Objects of class regulon. However, it also works if you provide this list to the argument regulon

justinjacobse commented 3 years ago

Thanks Christian, than my problem must lie somewhere in viper, I will go have a look at what's going on there.