generate_DSSignalingBase {pwOmics} | R Documentation |
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.
generate_DSSignalingBase(data_omics, timepoints = c(0.25, 1, 4, 8, 13, 18, 24))
data_omics |
OmicsData object. |
timepoints |
integer vector specifying the timepoints of interest for downstream analysis. |
Folder structure in working directory, containing phosphoprotein downstream information in individual folders.
## 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)