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saezlab / transcriptutorial

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
https://saezlab.github.io/transcriptutorial/
GNU General Public License v3.0
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Got a problem using assignPROGENYScores #45

Closed Holmes815 closed 1 year ago

Holmes815 commented 1 year ago

Hi, i´m using CARNIVAL to infer the network of reuglation in my scRNAseq data, i obtained my progeny results following this tutorial: https://saezlab.github.io/progeny/articles/ProgenySingleCell.html

The dataframe that i use is basically a dataframe with the pathways and scores inferred by progeny after using the prevously mentioned tutorial (just like the csv that is used in the chapter 05 of transcriptutorial) but this error keeps poping:

Error in progenyMembers[[which(names(progenyMembers) == pathways[ii])]] : attempt to select less than one element in get1index

I dont know what else to do, thanks in advance for the attention.

adugourd commented 1 year ago

Hi,

you can try to chek what are the pathway names in pathways[ii] if they match the names of the progeny members you get with names(progenyMembers)

However, we haven't tested carnival with single cell data yet, the tool was really intended for such a setting. I would at least avoid using progeny pathway to run carnival from single cell.