identifyPWTFTGs: Identify TFs in pathways and their target genes - downstream...

In pwOmics: Pathway-based data integration of omics data

Description

This function identifies the transcription factors being part of the pathways of downstream analysis. Subsequently it finds the target genes of these transcription factors from the selected TF-target gene database.

Usage

identifyPWTFTGs(data_omics, updown = FALSE)

Arguments

data_omics	OmicsData object.
updown	boolean value; TRUE in case up- and downregulation should be checked individually for intersection; FALSE = default, if only deregulation should be checked for.

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

## 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"))
data_omics_plus = identifyPR(data_omics_plus)
setwd(system.file("extdata/Genelists", package = "pwOmics.newupdown"))

## End(Not run)
## Not run: 
data_omics = identifyPWs(data_omics_plus)
data_omics = identifyTFs(data_omics)
data_omics = identifyPWTFTGs(data_omics)

## End(Not run)

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