getTFIntersection: Get TF intersection for the omics data on the different time...

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

Description

Get TF intersection for the omics data on the different time points.

Usage

getTFIntersection(data_omics, tp_prot, tp_genes, updown = FALSE,
  phospho = TRUE)

Arguments

data_omics	OmicsData object.
tp_prot	numeric integer defining protein timepoint measurement chosen for comparison.
tp_genes	numeric integer defining gene/transcript timepoint measurement chosen for comparison.
updown	boolean value; TRUE in case up- and downregulation should be checked individually for intersection. Type of checking is defined with parameter 'phospho'.
phospho	boolean value; TRUE in case up- and downregulation should be checked based on provided downstream phosphoprotein influence from identifyPR function; FALSE in case up- and downregulation should be checked for without phosphoprotein database knowledge. Default is TRUE.

Value

list with three elements: 1) character vector of transcription factor IDs identified in both upstream and downstream analysis 2) protein time point 3) gene/transcript time point.

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 = identifyPWTFTGs(data_omics)
data_omics = identifyRsofTFs(data_omics, noTFs_inPW = 1, order_neighbors = 10)
getTFIntersection(data_omics, tp_prot = 4, tp_genes = 4, updown = FALSE, 
phospho = TRUE)

## End(Not run)

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