search

ventolab / CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
https://www.cellphonedb.org/
MIT License
320 stars 51 forks source link

Clarification Needed on --threshold Argument #145

Closed macelik closed 11 months ago

macelik commented 11 months ago

Hello,

I have a clarification question about the --threshold argument. The documentation states that it represents a percentage of cells, but in the tutorial, it seems to be treated as a fraction. Could you clarify whether setting the threshold to 0.1 means 0.1% or 10%?

Thank you, Muhammet

datasome commented 11 months ago

Hi Muhammet, Thank you for using CellphoneDB. In https://cellphonedb.readthedocs.io/en/latest/RESULTS-DOCUMENTATION.html#analysis-methods please see the following:

1. all the genes in the interaction are expressed in the corresponding cell type by more than 10% of cells (threshold = 0.1)

That is threshold = 0.1 corresponds to/means 10% of cells. Hope that helps.

Best,

Robert.

macelik commented 11 months ago

Thank you for clearing that up. This resolves the confusion on my side, so I'm closing it now. I appreciate the prompt response.