nichenet_gr_network {OmnipathR} | R Documentation |
Builds gene regulatory network prior knowledge for NicheNet using multiple resources.
nichenet_gr_network( omnipath = list(), harmonizome = list(), regnetwork = list(), htridb = list(), remap = list(), evex = list(), pathwaycommons = list(), trrust = list(), only_omnipath = FALSE )
omnipath |
List with paramaters to be passed to
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harmonizome |
List with paramaters to be passed to
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regnetwork |
List with paramaters to be passed to
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htridb |
List with paramaters to be passed to
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remap |
List with paramaters to be passed to
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evex |
List with paramaters to be passed to
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pathwaycommons |
List with paramaters to be passed to
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trrust |
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 gene regulatory interactions suitable for use with NicheNet.
# load everything with the default parameters: gr_network <- nichenet_gr_network() # less targets from ReMap, not using RegNetwork: gr_network <- nichenet_gr_network( # I needed to disable ReMap here due to some issues # of one of the Bioconductor build servers # remap = list(top_targets = 200), remap = NULL, regnetwork = NULL, ) # use only OmniPath: gr_network_omnipath <- nichenet_gr_network(only_omnipath = TRUE)