findSignalingAxes {pwOmics} | R Documentation

## Find downstream signaling axis.

### Description

This function determines the regulated downstream structures of a selected phosphoprotein at a specified time point.

### Usage

    findSignalingAxes(data_omics, phosphoprot, tpDS)

### Arguments

`data_omics` | OmicsData object.
`phosphoprot` | character specifying the name of the phosphoprotein that is selected as the starting point for downstream analysis.
`tpDS` | integer specifying the time point considered for downstream analysis of phosphoprotein data .

### Value

list of downstream pathways identified for this time point of phosphoprotein measurement with sublists containing information about the transcription factor, the regulation, the target genes of these transcription factors and the matching transcripts.

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

    ## End(Not run)
    ## Not run:
    data_omics_plus = identifyPR(data_omics_plus)
    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)
    SYK_axis = findSignalingAxes(data_omics,phosphoprot = "SYK", tpDS = 2)

    ## End(Not run)

[Package pwOmics version 1.16.0 Index]