bnClustOmics (version 1.1.1)

annotateEdges: Annotating edges from discovered networks

Description

This function makes a data frame which contains all pairs of nodes connected in cluster-specific networks

Usage

annotateEdges(
  bnres,
  bnnames,
  sump = 1.2,
  minp = 0.5,
  minkp = 0.9,
  maxkp = NULL,
  dblist = NULL
)

Value

returns a data frame where each filteres interaction is annotated with IDs of omics variables, omics types, posterior probabilities of the interaction in the discovred clusters and a flag indication if the interaction could be found in the interaction data base

Arguments

bnres

an object of class 'bnclustOmics'; see bnclustOmics

bnnames

an object of class 'bnInfo'; see bnInfo

sump

threshold for the sum of posterior probabilities in all discovered networks

minp

threshold for the minimum posterior probability in at least one network, when the sum of posterioirs is bigger than sump

minkp

threshold for the minimum posterior probability in at least one network, when the sum of posterioirs is less than sump

maxkp

(optional) threshold for the maximum posterior probability in at least one network; used to esclude cluster specific edges from the edges with high sum of posterioirs (>sump)

dblist

a list of known interactions, discovered edges will be annotated is the edge is present in this list; two columns must be present 'gene1' and 'gene2'

Examples

bnnames<-bnInfo(simdata,c("b","c"),c("M","T"))
intlist<-annotateEdges(bnres3,bnnames,dblist=simint)
length(which(intlist$db))