## ----eval=FALSE--------------------------------------------------------------------------------------------- # library(OmnipathR) # library(nichenetr) # # nichenet_results <- nichenet_main( # expressed_genes_transmitter = expressed_genes_transmitter, # expressed_genes_receiver = expressed_genes_receiver, # genes_of_interest = genes_of_interest, # background_genes = background_genes, # signaling_network = list( # cpdb = NULL, # evex = list(min_confidence = 1.0) # ), # gr_network = list(only_omnipath = TRUE), # n_top_ligands = 20, # mlrmbo_optimization_param = list(ncores = 4) # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # nichenet_model <- nichenet_main() ## ----eval=FALSE--------------------------------------------------------------------------------------------- # require(devtools) # install_github('saeyslab/nichenetr') ## ----eval=FALSE--------------------------------------------------------------------------------------------- # library(nichenetr) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # nichenet_workarounds() ## ----eval=FALSE--------------------------------------------------------------------------------------------- # require(OmnipathR) # nichenet_workarounds() # nichenet_test() ## ----eval=FALSE--------------------------------------------------------------------------------------------- # networks <- nichenet_networks() ## ----eval=FALSE--------------------------------------------------------------------------------------------- # networks <- nichenet_networks(only_omnipath = TRUE) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # networks <- nichenet_networks( # only_omnipath = TRUE, # signaling_network = list( # omnipath = list( # resources = c('SIGNOR', 'PhosphoSite') # ) # ), # lr_network = list( # omnipath = list( # transmitter_param = list(parent = c('ligand', 'secreted_enzyme')), # receiver_param = list(parent = c('receptor', 'transporter')) # ) # ), # gr_network = list( # omnipath = list( # resources = 'DoRothEA', # dorothea_levels = 'A' # ) # ) # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # signaling_network <- nichenet_signaling_network( # cpdb = list( # complex_max_size = 1, # min_score = .98 # ), # evex = list( # min_confidence = 2 # ), # pathwaycommons = NULL # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # evex_signaling <- nichenet_signaling_network_evex(top_confidence = .9) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # evex <- evex_download(remove_negatives = FALSE) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # nichenet_results <- nichenet_main( # quality_filter_param = list( # min_curation_effort = 1, # consensus_percentile = 30 # ) # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # nichenet_results <- nichenet_main(small = TRUE) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # expression <- nichenet_expression_data() ## ----eval=FALSE--------------------------------------------------------------------------------------------- # lr_network <- nichenet_lr_network() # expression <- nichenet_remove_orphan_ligands( # expression = expression, # lr_network = lr_network # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # optimization_results <- nichenet_optimization( # networks = networks, # expression = expression, # mlrmbo_optimization_param = list(ncores = 4) # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # options(omnipath.nichenet_results_dir = 'my/nichenet/dir') # nichenet_results_dir() # # [1] "my/nichenet/dir" ## ----eval=FALSE--------------------------------------------------------------------------------------------- # nichenet_model <- nichenet_build_model( # optimization_results = optimization_results, # networks = networks, # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # lt_matrix <- nichenet_ligand_target_matrix( # nichenet_model$weighted_networks, # networks$lr_network, # nichenet_model$optimized_parameters # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # genes_of_interest <- sample(rownames(ligand_target_matrix), 50) # background_genes <- setdiff( # rownames(ligand_target_matrix), # genes_of_interest # ) # expressed_genes_transmitter <- union( # unlist(purrr::map(networks, 'from')), # unlist(purrr::map(networks, 'to')) # ) # expressed_genes_receiver <- expressed_genes_transmitter # # ligand_activities <- nichenet_ligand_activities( # ligand_target_matrix = lt_matrix, # lr_network = networks$lr_network, # expressed_genes_transmitter = expressed_genes_transmitter, # expressed_genes_receiver = expressed_genes_receiver, # genes_of_interest = genes_of_interest # ) ## ----eval=FALSE--------------------------------------------------------------------------------------------- # lt_links <- nichenet_ligand_target_links( # ligand_activities = ligand_activities, # ligand_target_matrix = lt_matrix, # genes_of_interest = genes_of_interest, # n_top_ligands = 20, # n_top_targets = 100 # ) ## ----sessionInfo, echo=FALSE-------------------------------------------------------------------------------- sessionInfo()