identifyPWTFTGs {pwOmics} | R Documentation

## Identify TFs in pathways and their target genes - downstream analysis.

### Description

This function identifies the transcription factors being part of the pathways of downstream analysis. Subsequently it finds the target genes of these transcription factors from the selected TF-target gene database.

### Usage

    identifyPWTFTGs(data_omics, updown = FALSE)

### Arguments

`data_omics` | OmicsData object.
`updown` | boolean value; TRUE in case up- and downregulation should be checked individually for intersection; FALSE = default, if only deregulation should be checked for.

### 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"))
    data_omics_plus = identifyPR(data_omics_plus)
    setwd(system.file("extdata/Genelists", package = "pwOmics.newupdown"))

    ## End(Not run)
    ## Not run:
    data_omics = identifyPWs(data_omics_plus)
    data_omics = identifyTFs(data_omics)
    data_omics = identifyPWTFTGs(data_omics)

    ## End(Not run)

[Package pwOmics version 1.22.0 Index]