generate_DSSignalingBase {pwOmics} | R Documentation

## Generate a folder with downstream information about all phosphoproteins.

### Description

This function generates a folder structure with an RData object and csv tables for each timepoint sepcified for each phosphoprotein considered in the data_omics object.

### Usage

    generate_DSSignalingBase(data_omics, timepoints = c(0.25, 1, 4, 8, 13, 18,
      24))

### Arguments

`data_omics` | OmicsData object.
`timepoints` | integer vector specifying the timepoints of interest for downstream analysis.

### Value

Folder structure in working directory, containing phosphoprotein downstream information in individual folders.

### 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)
    setwd("~/Signaling_axes/")
    generate_DSSignalingBase(data_omics, timepoints = c(0.25, 1, 4, 8, 13, 18, 24))

    ## End(Not run)

[Package pwOmics version 1.14.0 Index]