filterNetwork {GeneNetworkBuilder} | R Documentation

## 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)

[Package GeneNetworkBuilder version 1.30.0 Index]