findSignalingAxes: Find downstream signaling axis.

In pwOmics: Pathway-based data integration of omics data

Description

This function determines the regulated downstream structures of a selected phosphoprotein at a specified time point.

Usage

findSignalingAxes(data_omics, phosphoprot, tpDS)

Arguments

data_omics	OmicsData object.
phosphoprot	character specifying the name of the phosphoprotein that is selected as the starting point for downstream analysis.
tpDS	integer specifying the time point considered for downstream analysis of phosphoprotein data .

Value

list of downstream pathways identified for this time point of phosphoprotein measurement with sublists containing information about the transcription factor, the regulation, the target genes of these transcription factors and the matching transcripts.

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

## End(Not run)
## Not run: 
data_omics_plus = identifyPR(data_omics_plus)
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)
SYK_axis = findSignalingAxes(data_omics,phosphoprot = "SYK", tpDS = 2)

## End(Not run)

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