annotateEdges: Annotating edges from discovered networks

In bnClustOmics: Bayesian Network-Based Clustering of Multi-Omics Data

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
)

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'

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

Examples

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

bnClustOmics documentation built on Aug. 5, 2022, 5:11 p.m.