get_matching_transcripts: Summarize table of matching downstream transcripts.

In pwOmics: Pathway-based data integration of omics data

Description

This function returns the summarized table of matching transcripts information based on the result list from the findSignalingAxes function.

Usage

get_matching_transcripts(data_omics, axis)

Arguments

data_omics	OmicsData object.
axis	list output of findSignalingAxes.

Value

dataframe containing the target genes of the axis matching the transcript data in at least one of the time points in the first column, the direction of their regulation inferred from the phosphoproteome data in the second column, the transcript regulation in the next columns (per time point) and the summarized matched information in the following columns (per time point).

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"))

## 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 = identifyPWTFTGs(data_omics)
data_omics = identifyRsofTFs(data_omics, noTFs_inPW = 1, order_neighbors = 10)
SYK_axis = findSignalingAxes(data_omics,phosphoprot = "SYK", tpDS = 2)
SYK_transcripts = get_matching_transcripts(data_omics, SYK_axis)

## End(Not run)

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