filterNetwork: filter the regulatory network table by expression profile

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

filter the regulatory network table by expression profile

Description

verify every nodes in the regulatory network by expression profile

Usage

filterNetwork(
  rootgene,
  sifNetwork,
  exprsData,
  mergeBy = "symbols",
  miRNAlist,
  remove_miRNA = FALSE,
  tolerance = 0,
  cutoffPVal = 0.01,
  cutoffLFC = 0.5,
  minify = TRUE,
  miRNAtol = FALSE
)

Arguments

rootgene	name of root gene. It must be the ID used in xx regulatory network
sifNetwork	Transcription regulatory network table. Column names of xx must be 'from','to'
exprsData	dataset of expression comparison data, which should contain column logFC and column given by exprsDataByName
mergeBy	The column name contains ID information used to merge with 'to' column of sifNetwork in exprsData
miRNAlist	vector of microRNA ids.
remove_miRNA	remove miRNA from the network or not. Bool value, TRUE or FALSE
tolerance	maximum number of unverified nodes in each path
cutoffPVal	cutoff p value of valid differential expressed gene/miRNA
cutoffLFC	cutoff log fold change value of a valid differential expressed gene/miRNA
minify	Only keep the best path if multiple paths exists for single node? Bool value, TRUE or FALSE
miRNAtol	take miRNA expression into account for tolerance calculation. Bool value, TRUE or FALSE

Value

a dataframe of filtered regulatory network by expression profile

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)

jianhong/GeneNetworkBuilder documentation built on Nov. 4, 2024, 5:54 a.m.