identifyRsofTFs: Identify regulators of transcription factors - upstream...

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

Description

This function identifies the regulators upstream of the identified transcription factors in upstream analysis. Converting the pathway information to a regulatory graph needs some time... Warnings regarding the skipping of edges in building the regulatory graph can be ignored.

Usage

identifyRsofTFs(data_omics, noTFs_inPW = 2, order_neighbors = 6)

Arguments

data_omics	OmicsData object.
noTFs_inPW	integer; only regulators in upstream pathways with more than this number of TFs are identified.
order_neighbors	integer specifiying the order of the neighborhood: order 1 is TF plus its immediate neighbors.

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")) 
## 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)
setwd(system.file("extdata/Genelists", package = "pwOmics"))
data_omics = identifyRsofTFs(data_omics, 
noTFs_inPW = 1, order_neighbors = 10)

## End(Not run)

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