NicheNet gene regulatory network from EVEX — nichenet_gr_network_evex • OmnipathR

Builds a gene regulatory network using data from the EVEX database and converts it to a format suitable for NicheNet.

Usage

nichenet_gr_network_evex(
  top_confidence = 0.75,
  indirect = FALSE,
  regulation_of_expression = FALSE
)

Arguments

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.

Value

Data frame of interactions in NicheNet format.

Data frame with gene regulatory interactions in NicheNet format.

See also

nichenet_gr_network
evex_download

Examples

# use only the 10% with the highest confidence:
evex_gr_network <- nichenet_gr_network_evex(top_confidence = .9)