NicheNet gene regulatory network from ReMap — nichenet_gr_network_remap • OmnipathR

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

Usage

nichenet_gr_network_remap(
  score = 100,
  top_targets = 500,
  only_known_tfs = TRUE
)

Arguments

score: Numeric: a minimum score between 0 and 1000, records with lower scores will be excluded. If NULL no filtering performed.
top_targets: Numeric: the number of top scoring targets for each TF. Essentially the maximum number of targets per TF. If NULL the number of targets is not restricted.
only_known_tfs: Logical: whether to exclude TFs which are not in TF census.

Value

Data frame with gene regulatory interactions in NicheNet format.

See also

remap_filtered
nichenet_gr_network

Examples

# use only max. top 100 targets for each TF:
remap_gr_network <- nichenet_gr_network_remap(top_targets = 100)