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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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running runGenie3 using a custom list of TFs #114

Closed arijita88 closed 2 years ago

arijita88 commented 4 years ago

Hi, How can I run runGenie3 using a custom list of transcription factors(TFs)? For example, as mentioned in the GENIE3 vignette, it can be done using regulators <- c("Gene1", "Gene2", "Gene3") and then weightMat <- GENIE3(exprMatr, regulators=regulators). My .loom file is huge and runGenie3 detects 1286 TFs in it. I need to run the .loom file just for 10 TFs. Any advice on this will be really helpful. Thank you.

jonesphil93 commented 3 years ago

Hi!

Did you figure out how to solve this problem? I would also like to use some TFs as regulators, but haven't found a solution to this problem yet... Thanks!

arijita88 commented 3 years ago

Hi, Sorry I haven't found a solution to this problem yet. I really want to figure out how to do this. Please let me know if you have any leads on this.

Thank You Arijita

On Thu, Oct 22, 2020 at 7:18 AM jonesphil93 notifications@github.com wrote:

Hi!

Did you figure out how to solve this problem? I would also like to use some TFs as regulators, but haven't found a solution to this problem yet... Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/aertslab/SCENIC/issues/114#issuecomment-714526567, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIGZZBALIOZ2ZHJ6LABXEHLSMA5KPANCNFSM4KEAVOCA .

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Arijita Sarkar University of Southern California Department of Orthopaedic Surgery Stem Cell Research and Regenerative Medicine Evseenko Lab 1450 Biggy St. NRT4509 Los Angeles, CA 90033 arijitas@usc.edu

s-aibar commented 3 years ago

Dear @arijita88 and @jonesphil93 ,

I have added the option to select the input TFs to the runGenie3 function (argument allTFs).

However, beware that using only a small subset of TFs will modify the results of the pipeline! Keep in mind that this isn't a supported modification, so you should probably test it yourself: for example, keep at least a few extra TFs as negative controls, and also check that the thresholds for creating the co-expression modules still make sense (i.e. manually run the vignette detailedStep_1_coexNetwork2modules.Rmd, to confirm everything is fine... )

jonesphil93 commented 3 years ago

Dear @s-aibar ,

thank you very much for your help and efforts!

Sorry for being so stupid, but you provide an example how to use the allTFs argument? E.g., if I want to run it for example only for the TFs Id2 and Prdm1 (because they are highly expressed in my dataset) and use Bcl6 as negative control, what will my argument allTFs look like?

Thank you very much!

s-aibar commented 3 years ago

Just provide them all as a vector:

e.g.: allTFs=c("Id2", "Prdm1", "Bcl6")

jonesphil93 commented 3 years ago

Thanks!

arijita88 commented 3 years ago

Hi @s-aibar https://github.com/s-aibar, Thank you so much for helping us with this.

On Fri, Oct 23, 2020 at 6:18 AM jonesphil93 notifications@github.com wrote:

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/aertslab/SCENIC/issues/114#issuecomment-715335361, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIGZZBEMLB4QQXOYXMNVWQLSMF7DNANCNFSM4KEAVOCA .

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Arijita Sarkar University of Southern California Department of Orthopaedic Surgery Stem Cell Research and Regenerative Medicine Evseenko Lab 1450 Biggy St. NRT4509 Los Angeles, CA 90033 arijitas@usc.edu