Hi,
SCENIC is a great tool. I used pySCENIC to get the binarization matrix result. And follow the workflow in R http://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/inst/doc/SCENIC_Running.html
In the end of SCENIC workflow on this website, I follow the 'Binarized version' and get the heatmap. But when I set the parameter minPerc to 0.7, there is few transcription factors remain. I wonder could I lower this parameter or remove this parameter and just get the matrix with this code:binaryActPerc_subset <- regulonActivity_byCellType_Binarized[which(rowSums(regulonActivity_byCellType_Binarized)>0),]
This would lead to more TFs for the next analysis.Is this reasonable?
Thanks for any team member's response!
Hi, SCENIC is a great tool. I used pySCENIC to get the binarization matrix result. And follow the workflow in R http://htmlpreview.github.io/?https://github.com/aertslab/SCENIC/blob/master/inst/doc/SCENIC_Running.html In the end of SCENIC workflow on this website, I follow the 'Binarized version' and get the heatmap. But when I set the parameter minPerc to 0.7, there is few transcription factors remain. I wonder could I lower this parameter or remove this parameter and just get the matrix with this code:binaryActPerc_subset <- regulonActivity_byCellType_Binarized[which(rowSums(regulonActivity_byCellType_Binarized)>0),] This would lead to more TFs for the next analysis.Is this reasonable? Thanks for any team member's response!