identifyPR {pwOmics} | R Documentation

## Identify phosphorylation regulation influence downstream

### Description

This function identifies the downstream regulation influence of phosphoprotein regulation for further downstream analysis steps.

### Usage

    identifyPR(data_omics_plus)

### Arguments

`data_omics_plus` | output list of readPWdata function; first element contains an OmicsData object, secons element the genelist data corresponding to the selected pathway database.

### 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)

    ## End(Not run)

[Package pwOmics version 1.22.0 Index]