temp_correlations {pwOmics} | R Documentation |
This function plots an overview of consensus phosphoprotein expression level correlations with those transcripts that are affected downstream in a newly generated folder in the working directory. The following additional information needs to be provided: Phosphorylation information amino acid, position and multiplicity with the expression levels for each of the time points the correlations should be plotted for. Furthermore data tables for fold changes/ratios of phosphoproteins and transcripts that are part of the data_omics object.
temp_correlations(ConsensusGraph, timepointsprot, timepointstrans, foldername = "ProtCons_", trans_sign = "signif_single.csv", trans_sign_names, phospho_sign = "mat_phospho.csv", phospho_sign_names)
ConsensusGraph |
result from static analysis: consensus graph generated by staticConsensusNet function. |
timepointsprot |
numeric vector with measurement time points in phosphoproteome data set, which should be used for correlation plots |
timepointstrans |
numeric vector with measurement time points in transcriptome data set, which should be used for correlation plots |
foldername |
character vector specifying the name of the folder that will be generated for the temporal correlations |
trans_sign |
character vector specifying a tab-delimited file with the transcriptome expression levels for all time points in timepointstrans |
trans_sign_names |
character vector specifying column names in the transcriptome file corresponding to the expression levels at different time points. |
phospho_sign |
character vector specifying a tab-delimited file with the phosphoproteome information (columns 'Gene.names', 'Amino.acid', 'Position', 'Multiplicity') and expression levels for all time points in timepointstrans |
phospho_sign_names |
character vector specifying column names in the phosphoproteome file corresponding to the expression levels at different time points. |
... |
further plotting/legend parameters. |
pdf file in current working directory.
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")) ## Not run: data_omics_plus = identifyPR(data_omics_plus) 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) data_omics = identifyPWTFTGs(data_omics) statConsNet = staticConsensusNet(data_omics) temp_correlations(statConsNet, timepointsprot = c(1,4,8,13,18,24), timepointstrans = c(1,4,8,13,18,24), foldername = "ProtCons_", trans_sign = system.file("extdata", "signif_single.csv", package = "pwOmics") trans_sign_names = c("FC_1", "FC_2", "FC_3", "FC_4"), phospho_sign = system.file("extdata", "mat_phospho.csv", package = "pwOmics") phospho_sign_names = c("Rat1", "Rat2", "Rat3", "Rat4")) ) ## End(Not run)