tcss_cutoff {GOSemSim} | R Documentation |
determine the topological cutoff for TCSS method
tcss_cutoff( OrgDb = NULL, keytype = "ENTREZID", ont, combine_method = "max", ppidata )
OrgDb |
OrgDb object |
keytype |
keytype |
ont |
ontology : "BP", "MF", "CC" |
combine_method |
"max", "BMA", "avg", "rcmax", "rcmax.avg" |
ppidata |
A data.frame contains positive set and negative set. Positive set is PPI pairs that already verified. ppidata has three columns, column 1 and 2 are character, column 3 must be logical value:TRUE/FALSE. |
numeric, topological cutoff for given parameters
## Not run: library(org.Hs.eg.db) library(STRINGdb) string_db <- STRINGdb$new(version = "11.0", species = 9606, score_threshold = 700) string_proteins <- string_db$get_proteins() #get relationship ppi <- string_db$get_interactions(string_proteins$protein_external_id) ppi$from <- vapply(ppi$from, function(e) strsplit(e, "9606.")[[1]][2], character(1)) ppi$to <- vapply(ppi$to, function(e) strsplit(e, "9606.")[[1]][2], character(1)) len <- nrow(ppi) #select length s_len <- 100 pos_1 <- sample(len, s_len, replace = T) #negative set pos_2 <- sample(len, s_len, replace = T) pos_3 <- sample(len, s_len, replace = T) #union as ppidata ppidata <- data.frame(pro1 = c(ppi$from[pos_1], ppi$from[pos_2]), pro2 = c(ppi$to[pos_1], ppi$to[pos_3]), label = c(rep(TRUE, s_len), rep(FALSE, s_len)), stringsAsFactors = FALSE) cutoff <- tcss_cutoff(OrgDb = org.Hs.eg.db, keytype = "ENSEMBLPROT", ont = "BP", combine_method = "max", ppidata) ## End(Not run)