getGenesIntersection {pwOmics} | R Documentation |
Get genes intersection for the omics data on the different time points.
getGenesIntersection(data_omics, tp_prot, tp_genes, updown = FALSE, phospho = TRUE)
data_omics |
OmicsData object. |
tp_prot |
numeric integer defining protein timepoint measurement chosen for comparison. |
tp_genes |
numeric integer defining gene/transcript timepoint measurement chosen for comparison. |
updown |
boolean value; TRUE in case up- and downregulation should be checked individually for intersection. Type of checking is defined with parameter 'phospho'. |
phospho |
boolean value; TRUE in case up- and downregulation should be checked based on provided downstream phosphoprotein influence from identifyPR function; FALSE in case up- and downregulation should be checked for without phosphoprotein database knowledge. Default is TRUE. |
list with three elements: 1) character vector of gene IDs identified in both upstream and downstream analysis 2) protein time point 3) gene/transcript time point.
## 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) getGenesIntersection(data_omics, tp_prot = 4, tp_genes = 4, updown = FALSE, phospho = TRUE) ## End(Not run)