nichenet_lr_network_omnipath {OmnipathR} | R Documentation |
Retrieves network prior knowledge from OmniPath and provides it in
a format suitable for NicheNet.
This method never downloads the 'ligrecextra' dataset because the
ligand-receptor interactions are supposed to come from
nichenet_lr_network_omnipath
.
nichenet_lr_network_omnipath(quality_filter_param = list(), ...)
quality_filter_param |
List with arguments for |
... |
Passed to |
A network data frame (tibble) with ligand-receptor interactions suitable for use with NicheNet.
# use only ligand-receptor interactions (not for example ECM-adhesion): op_lr_network <- nichenet_lr_network_omnipath(ligand_receptor = TRUE) # use only CellPhoneDB and Guide to Pharmacology: op_lr_network <- nichenet_lr_network_omnipath( resources = c('CellPhoneDB', 'Guide2Pharma') ) # only interactions where the receiver is a transporter: op_lr_network <- nichenet_lr_network_omnipath( receiver_param = list(parent = 'transporter') )