infoConsensusGraph: Add Consensus Graph information.

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

Description

Adds phosphoprotein information based on phosphoprotein data table and redraws Consensus Graph edges

Usage

infoConsensusGraph(data_omics, consensusGraph, phosphotab)

Arguments

data_omics	OmicsData object.
consensusGraph	result from static analysis: consensus graph generated by staticConsensusNet function.
phosphotab	dataframe with phosphoprotein information annotated in columns 'Gene.names', 'Amino acid', 'Position' (of phosphosite).

Value

graph of igraph class containing complemented consensus graph information

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")) 
## Not run: 
data_omics_plus = identifyPR(data_omics_plus) 
setwd(system.file("extdata/Genelists", package = "pwOmics"))
data_omics = identifyPWs(data_omics_plus)
data_omics = identifyTFs(data_omics)
data_omics = identifyRsofTFs(data_omics, 
noTFs_inPW = 1, order_neighbors = 10)
data_omics = identifyPWTFTGs(data_omics)
statConsNet = staticConsensusNet(data_omics)

## End(Not run)

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