infoConsensusGraph: Add Consensus Graph information.

Description Usage Arguments Value Examples

View source: R/pwOmics_consensus_analysis.R

Description

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

Usage

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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

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## 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 = identifyRsofTFs(data_omics, 
noTFs_inPW = 1, order_neighbors = 10)
data_omics = identifyPWTFTGs(data_omics)
statConsNet = staticConsensusNet(data_omics)

## End(Not run)

pwOmics documentation built on Nov. 8, 2020, 4:55 p.m.