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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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A question about Regulon format #4

Closed andreyurch closed 4 years ago

andreyurch commented 5 years ago

Dear developers,

Is there a way to make a regulon object based on my specific set of TF and their targets?

Thank you!

christianholland commented 5 years ago

Dear user,

thanks for your question. Yes, this is possible. However, there is no dedicated function for this and of course the required steps depends on your current data format. If you want to provide your current format I can help you with converting it to a regulon object.

Best, Christian

EDIT: Just saw that you opened the issue 23 days ago. Apologise the late reply. For some reason I didn't receive a notification

andreyurch commented 5 years ago

Dear Christian,

Thank you for your reply! I like very much the Dorothea idea and database. I actually take the regulons from your repository http://saezlab.org/tfregulons/ and format it removing some interactions or adding them (activation, repression). So, it would be great to find a way to convert from this format or from https://github.com/saezlab/DoRothEA/tree/master/data/TFregulons/consensus/table to VIPER.

By the way, can I ask what is the publication stage of your paper https://www.biorxiv.org/content/10.1101/337915v2 ?

Best, Andrey

christianholland commented 5 years ago

Hi Andrey, you can use the function df2regulon() which you find here. This function was designed to transform regulons stored as data frame to the required viper format. The data frame must exclusively contain the following columns: tf, target, mor, likelihood. Please let me know if something doesn't work.

The paper is in second revision, so we hope that it will be published very soon.

Best, Christian