readPhosphodata: Reads in phosphoprotein downstream regulation information.

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

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

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")) 

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