getUS_PWs: Get upstream pathways of identified transcription factors.

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

Description

Get upstream pathways of identified transcription factors.

Usage

getUS_PWs(data_omics)

Arguments

data_omics

OmicsData object.

Value

list of length = number of gene/transcript time points, each element containing a list of transcription factors; these transcription factor elements contain data frame with pathway IDs and pathway names.

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"))
data_omics_plus = identifyPR(data_omics_plus)
## Not run: 
setwd(system.file("extdata/Genelists", package = "pwOmics"))
data_omics = identifyPWs(data_omics_plus)
data_omics = identifyTFs(data_omics)
data_omics = identifyRsofTFs(data_omics, 
noTFs_inPW = 1, order_neighbors = 10)
getUS_PWs(data_omics)

## End(Not run)

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