identifyPR: Identify phosphorylation regulation influence downstream

In MarenS2/pwOmics_maren: Pathway-based data integration of omics data

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

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")) 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics"))
data_omics_plus = readPWdata(data_omics,  
loadgenelists = system.file("extdata/Genelists", package = "pwOmics"))
data_omics_plus = identifyPR(data_omics_plus)

MarenS2/pwOmics_maren documentation built on May 6, 2019, 3:27 p.m.