infoConsensusGraph {pwOmics} | R Documentation

## Add Consensus Graph information.

### Description

Adds phosphoprotein information based on phosphoprotein data table and redraws Consensus Graph edges

### Usage

    infoConsensusGraph(data_omics, consensusGraph, phosphotab)

### Arguments

`data_omics` | OmicsData object.
`consensusGraph` | result from static analysis: consensus graph generated by staticConsensusNet function.
`phosphotab` | dataframe with phosphoprotein information annotated in columns 'Gene.names', 'Amino acid', 'Position' (of phosphosite).

### Value

graph of igraph class containing complemented consensus graph information

### Examples

    ## Not run:
    data(OmicsExampleData)
    data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24),
    tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
    PWdatabase = c("biocarta", "kegg", "nci", "reactome"),
    TFtargetdatabase = c("userspec"))
    data_omics = readPhosphodata(data_omics,
    phosphoreg = system.file("extdata", "phospho_reg_table.txt",
    package = "pwOmics.newupdown"))
    data_omics = readTFdata(data_omics,
    TF_target_path = system.file("extdata", "TF_targets.txt",
    package = "pwOmics.newupdown"))
    data_omics_plus = readPWdata(data_omics,
    loadgenelists = system.file("extdata/Genelists", package = "pwOmics.newupdown"))

    ## End(Not run)
    ## Not run:
    data_omics_plus = identifyPR(data_omics_plus)
    setwd(system.file("extdata/Genelists", package = "pwOmics.newupdown"))
    data_omics = identifyPWs(data_omics_plus)
    data_omics = identifyTFs(data_omics)
    data_omics = identifyRsofTFs(data_omics,
    noTFs_inPW = 1, order_neighbors = 10)
    data_omics = identifyPWTFTGs(data_omics)
    statConsNet = staticConsensusNet(data_omics)

    ## End(Not run)

[Package pwOmics version 1.20.0 Index]