## ----------------------------------------------------------------------------- library(IMMAN) ## ----------------------------------------------------------------------------- data(FruitFly) data(Celegance) subFruitFly <- as.character(FruitFly$V1)[1:10] subCelegance <- as.character(Celegance$V1)[1:10] ## ----------------------------------------------------------------------------- ProteinLists = list(subFruitFly, subCelegance) List1_Species_ID = 7227 # taxonomy ID FruitFly List2_Species_ID = 6239 # taxonomy ID Celegance Species_IDs = c(List1_Species_ID, List2_Species_ID) ## ----------------------------------------------------------------------------- identityU = 30 substitutionMatrix = "BLOSUM62" gapOpening = -8 gapExtension = -8 NetworkShrinkage = FALSE coverage = 1 BestHit = TRUE score_threshold = 400 STRINGversion="11" ## ----------------------------------------------------------------------------- output = IMMAN(ProteinLists, fileNames=NULL, Species_IDs, identityU, substitutionMatrix, gapOpening, gapExtension, BestHit, coverage, NetworkShrinkage, score_threshold, STRINGversion, InputDirectory = getwd()) ## ----------------------------------------------------------------------------- output$IPNEdges output$IPNNodes output$Networks output$Networks[[1]] output$maps output$maps[[2]]