getProteinIntersection {pwOmics} | R Documentation

## Get protein intersection for the omics data on the different time points. The timepoints or measurement names for comparison have to be defined in tp_prot and tp_genes as given in the readOmics function.

### Description

Get protein intersection for the omics data on the different time points.

The timepoints or measurement names for comparison have to be defined in tp_prot and tp_genes as given in the readOmics function.

### Usage

    getProteinIntersection(data_omics, tp_prot, tp_genes, updown = FALSE,
      phospho = TRUE)

### Arguments

`data_omics` | OmicsData object.
`tp_prot` | numeric integer defining protein timepoint measurement chosen for comparison.
`tp_genes` | numeric integer defining gene/transcript timepoint measurement chosen for comparison.
`updown` | boolean value; TRUE in case up- and downregulation should be checked individually for intersection. Type of checking is defined with parameter 'phospho'.
`phospho` | boolean value; TRUE in case up- and downregulation should be checked based on provided downstream phosphoprotein influence from identifyPR function; FALSE in case up- and downregulation should be checked for without phosphoprotein database knowledge. Default is TRUE.

### Value

list with three elements: 1) character vector of protein IDs identified in both upstream and downstream analysis 2) protein time point 3) gene/transcript time point.

### 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 = identifyPWTFTGs(data_omics)
    data_omics = identifyRsofTFs(data_omics, noTFs_inPW = 1, order_neighbors = 10)
    getProteinIntersection(data_omics, tp_prot = 4, tp_genes = 4,
    updown = FALSE, phospho = TRUE)

    ## End(Not run)

[Package pwOmics version 1.14.0 Index]