polishNetwork {GeneNetworkBuilder} | R Documentation

## generate an object of grahpNEL to represent the regulation network

### Description

generate an object of grahpNEL to represent the regulation network. Each node will has three attributes: size, borderColor and fill.

### Usage

    polishNetwork(cifNetwork, nodesDefaultSize = 48,
      useLogFCAsWeight = FALSE, nodecolor = colorRampPalette(c("green",
      "yellow", "red"))(5), nodeBg = "white", nodeBorderColor = list(gene =
      "darkgreen", miRNA = "darkblue"), edgelwd = 0.25, ...)

### Arguments

`cifNetwork` | dataframe used to draw network graph. column names of cifNetwork must contain 'from', 'to', 'logFC' and 'miRNA'
`nodesDefaultSize` | nodes default size
`useLogFCAsWeight` | how to determine the weights for each nodes. If TURE, use logFC value as weight. If FALSE, use constant 1 as weight.
`nodecolor` | a character vector of color set. The node color will be mapped to color set by log fold change
`nodeBg` | background of node
`nodeBorderColor` | a list of broder node color set. nodeBorderColor's element must be gene and miRNA
`edgelwd` | the width of edge
`...` | any parameters can be passed to graph.par

### Value

An object of graphNEL class of the network

### Examples

    data("ce.miRNA.map")
    data("example.data")
    data("ce.interactionmap")
    data("ce.IDsMap")
    sifNetwork<-buildNetwork(example.data$ce.bind, ce.interactionmap, level=2)
    cifNetwork<-filterNetwork(rootgene=ce.IDsMap["DAF-16"], sifNetwork=sifNetwork,
      exprsData=uniqueExprsData(example.data$ce.exprData, "Max", condenseName='logFC'),
      mergeBy="symbols",
      miRNAlist=as.character(ce.miRNA.map[ , 1]), tolerance=1)
    gR<-polishNetwork(cifNetwork)
    ##	browseNetwork(gR)

[Package GeneNetworkBuilder version 1.28.1 Index]