generate_DSSignalingBase: Generate a folder with downstream information about all...

In pwOmics: Pathway-based data integration of omics data

Description

This function generates a folder structure with an RData object and csv tables for each timepoint sepcified for each phosphoprotein considered in the data_omics object.

Usage

generate_DSSignalingBase(data_omics, timepoints = c(0.25, 1, 4, 8, 13, 18,
  24))

Arguments

data_omics	OmicsData object.
timepoints	integer vector specifying the timepoints of interest for downstream analysis.

Value

Folder structure in working directory, containing phosphoprotein downstream information in individual folders.

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)
setwd("~/Signaling_axes/")
generate_DSSignalingBase(data_omics, timepoints = c(0.25, 1, 4, 8, 13, 18, 24))

## End(Not run)

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