filterNetwork: filter the regulatory network table by expression profile

Description Usage Arguments Value Examples

Description

verify every nodes in the regulatory network by expression profile

Usage

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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

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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)


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