nichenet_lr_network: Builds a NicheNet ligand-receptor network

In saezlab/OmnipathR: OmniPath web service client and more

Builds a NicheNet ligand-receptor network

Description

Builds ligand-receptor network prior knowledge for NicheNet using multiple resources.

Usage

nichenet_lr_network(
  omnipath = list(),
  guide2pharma = list(),
  ramilowski = list(),
  only_omnipath = FALSE,
  quality_filter_param = list()
)

Arguments

omnipath	List with paramaters to be passed to nichenet_lr_network_omnipath.
guide2pharma	List with paramaters to be passed to nichenet_lr_network_guide2pharma.
ramilowski	List with paramaters to be passed to nichenet_lr_network_ramilowski.
only_omnipath	Logical: a shortcut to use only OmniPath as network resource.
quality_filter_param	Arguments for filter_intercell_network (quality filtering of the OmniPath ligand-receptor network). It is recommended to check these parameters and apply some quality filtering. The defaults already ensure certain filtering, but you might want more relaxed or stringent options.

Value

A network data frame (tibble) with ligand-receptor interactions suitable for use with NicheNet.

See Also

• nichenet_lr_network_omnipath

• nichenet_lr_network_guide2pharma

• nichenet_lr_network_ramilowski

• filter_intercell_network

Examples

# load everything with the default parameters:
lr_network <- nichenet_lr_network()

# don't use Ramilowski:
lr_network <- nichenet_lr_network(ramilowski = NULL)

# use only OmniPath:
lr_network_omnipath <- nichenet_lr_network(only_omnipath = TRUE)

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.