identifyRsofTFs {pwOmics} | R Documentation |
This function identifies the regulators upstream of the identified transcription factors in upstream analysis. Converting the pathway information to a regulatory graph needs some time... Warnings regarding the skipping of edges in building the regulatory graph can be ignored.
identifyRsofTFs(data_omics, noTFs_inPW = 2, order_neighbors = 6)
data_omics |
OmicsData object. |
noTFs_inPW |
integer; only regulators in upstream pathways with more than this number of TFs are identified. |
order_neighbors |
integer specifiying the order of the neighborhood: order 1 is TF plus its immediate neighbors. |
OmicsData object: list of 4 elements (OmicsD, PathwayD, TFtargetsD, Status); OmicsD containing omics data set + results (after analysis); PathwayD containing selected pathway databases + biopax model; TFtargetsD containing selected TF target gene databases + TF target gene data.
## 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) setwd(system.file("extdata/Genelists", package = "pwOmics")) data_omics = identifyRsofTFs(data_omics, noTFs_inPW = 1, order_neighbors = 10) ## End(Not run)