identifyRsofTFs {pwOmics} | R Documentation

## Identify regulators of transcription factors - upstream analysis.

### Description

This function identifies the regulators upstream of the identified transcription factors in upstream analysis. Converting the pathway information to a regulatory graph needs some time... Warnings regarding the skipping of edges in building the regulatory graph can be ignored.

### Usage

    identifyRsofTFs(data_omics, noTFs_inPW = 2, order_neighbors = 6)

### Arguments

`data_omics` | OmicsData object.
`noTFs_inPW` | integer; only regulators in upstream pathways with more than this number of TFs are identified.
`order_neighbors` | integer specifiying the order of the neighborhood: order 1 is TF plus its immediate neighbors.

### Value

OmicsData object: list of 4 elements (OmicsD, PathwayD, TFtargetsD, Status); OmicsD containing omics data set + results (after analysis); PathwayD containing selected pathway databases + biopax model; TFtargetsD containing selected TF target gene databases + TF target gene data.

### 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)
    setwd(system.file("extdata/Genelists", package = "pwOmics"))
    data_omics = identifyRsofTFs(data_omics,
    noTFs_inPW = 1, order_neighbors = 10)

    ## End(Not run)

[Package pwOmics version 1.12.0 Index]