tcss_cutoff {GOSemSim} | R Documentation

## determine the topological cutoff for TCSS method

### Description

determine the topological cutoff for TCSS method

### Usage

    tcss_cutoff(
      OrgDb = NULL,
      keytype = "ENTREZID",
      ont,
      combine_method = "max",
      ppidata
    )

### Arguments

`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.

### Value

numeric, topological cutoff for given parameters

### Examples

    ## 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)

[Package GOSemSim version 2.20.0 Index]