nichenet_signaling_network: Builds a NicheNet signaling network
In saezlab/OmnipathR: OmniPath web service client and more

nichenet_signaling_network

R Documentation

Builds a NicheNet signaling network

Description

Builds signaling network prior knowledge for NicheNet using multiple resources.

Usage

nichenet_signaling_network(
  omnipath = list(),
  pathwaycommons = list(),
  harmonizome = list(),
  vinayagam = list(),
  cpdb = list(),
  evex = list(),
  inbiomap = list(),
  only_omnipath = FALSE
)

Arguments

`omnipath`	List with paramaters to be passed to `nichenet_signaling_network_omnipath`.
`pathwaycommons`	List with paramaters to be passed to `nichenet_signaling_network_pathwaycommons`.
`harmonizome`	List with paramaters to be passed to `nichenet_signaling_network_harmonizome`.
`vinayagam`	List with paramaters to be passed to `nichenet_signaling_network_vinayagam`.
`cpdb`	List with paramaters to be passed to `nichenet_signaling_network_cpdb`.
`evex`	List with paramaters to be passed to `nichenet_signaling_network_evex`.
`inbiomap`	List with paramaters to be passed to `nichenet_signaling_network_inbiomap`.
`only_omnipath`	Logical: a shortcut to use only OmniPath as network resource.

Value

A network data frame (tibble) with signaling interactions suitable for use with NicheNet.

Examples

# load everything with the default parameters:
# we don't load inBio Map due to the - hopefully
# temporary - issues of their server
sig_network <- nichenet_signaling_network(inbiomap = NULL, cpdb = NULL)

# override parameters for some resources:
sig_network <- nichenet_signaling_network(
    omnipath = list(resources = c('SIGNOR', 'SignaLink3', 'SPIKE')),
    pathwaycommons = NULL,
    harmonizome = list(datasets = c('phosphositeplus', 'depod')),
    # we can not include this in everyday tests as it takes too long:
    # cpdb = list(complex_max_size = 1, min_score = .98),
    cpdb = NULL,
    evex = list(min_confidence = 1.5),
    inbiomap = NULL
)

# use only OmniPath:
sig_network_omnipath <- nichenet_signaling_network(only_omnipath = TRUE)

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.