nichenet_signaling_network {OmnipathR} | R Documentation |
Builds signaling network prior knowledge for NicheNet using multiple resources.
nichenet_signaling_network( omnipath = list(), pathwaycommons = list(), harmonizome = list(), vinayagam = list(), cpdb = list(), evex = list(), inbiomap = list(), only_omnipath = FALSE )
omnipath |
List with paramaters to be passed to
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pathwaycommons |
List with paramaters to be passed to
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harmonizome |
List with paramaters to be passed to
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vinayagam |
List with paramaters to be passed to
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cpdb |
List with paramaters to be passed to
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evex |
List with paramaters to be passed to
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inbiomap |
List with paramaters to be passed to
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only_omnipath |
Logical: a shortcut to use only OmniPath as network resource. |
A network data frame (tibble) with signaling interactions suitable for use with NicheNet.
# 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) # 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')), cpdb = list(complex_max_size = 1, min_score = .98), evex = list(min_confidence = 1.5), inbiomap = NULL ) # use only OmniPath: sig_network_omnipath <- nichenet_signaling_network(only_omnipath = TRUE)