polishNetwork: generate an object of grahpNEL to represent the regulation...

In GeneNetworkBuilder: GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

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)

GeneNetworkBuilder documentation built on Nov. 8, 2020, 8:24 p.m.