readPhosphodata {pwOmics} | R Documentation

## Reads in phosphoprotein downstream regulation information.

### Description

This function reads in phosphoprotein downstream regulation information from a txt file.

### Usage

    readPhosphodata(data_omics, phosphoreg)

### Arguments

`data_omics` | OmicsData object.
`phosphoreg` | txt file with 2 columns, first providing gene names, second giving -1/1 annotation whether downstream regulation of phosphoprotein is inhibiting or activating, respectively.

### 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; PhosphoD containing optionally phosphoprotein downstream regulation annotation.

### 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"))

    ## End(Not run)

[Package pwOmics version 1.16.0 Index]