nichenet_gr_network_evex {OmnipathR} | R Documentation |
Builds a gene regulatory network using data from the EVEX database and converts it to a format suitable for NicheNet.
nichenet_gr_network_evex( top_confidence = 0.75, indirect = FALSE, regulation_of_expression = FALSE )
top_confidence |
Double, between 0 and 1. Threshold based on the quantile of the confidence score. |
indirect |
Logical: whether to include indirect interactions. |
regulation_of_expression |
Logical: whether to include also the "regulation of expression" type interactions. |
Data frame of interactions in NicheNet format.
Data frame with gene regulatory interactions in NicheNet format.
# use only the 10% with the highest confidence: evex_gr_network <- nichenet_gr_network_evex(top_confidence = .9)