easyTENET |
Run the step 1 through step 6 functions with default arguments |
humanTranscriptionFactorList |
Human transcription factor list |
step1MakeExternalDatasets |
Create a GRanges object representing putative regulatory element regions, based on the data sources selected for inclusion, to be used in later TENET steps |
step2GetDifferentiallyMethylatedSites |
Identify differentially methylated RE DNA methylation sites |
step3GetAnalysisZScores |
Calculate Z-scores comparing the mean expression of each gene in the case samples that are hyper- or hypomethylated for each RE DNA methylation site chosen in step 2 |
step4SelectMostSignificantLinksPerDNAMethylationSite |
Select the most significant RE DNA methylation site-gene links to each RE DNA methylation site |
step5OptimizeLinks |
Find final RE DNA methylation site-gene links using various optimization metrics |
step6DNAMethylationSitesPerGeneTabulation |
Tabulate the total number of RE DNA methylation sites linked to each of the genes |
step7ExpressionVsDNAMethylationScatterplots |
Create scatterplots displaying the expression of the top genes and the methylation levels of each of their linked RE DNA methylation sites, along with copy number variation, somatic mutation, and purity data, if provided by the user |
step7LinkedDNAMethylationSiteCountHistograms |
Create histograms displaying the number of genes or transcription factors linked to a given number of RE DNA methylation sites |
step7LinkedDNAMethylationSitesMotifSearching |
Perform motif searching for transcription factor motifs in the vicinity of RE DNA methylation sites linked to the specified transcription factors |
step7SelectedDNAMethylationSitesCaseVsControlBoxplots |
Generate boxplots comparing the methylation level of the specified RE DNA methylation sites in case and control samples |
step7StatesForLinks |
Identify which of the case samples harbor each of the identified regulatory element DNA methylation site-gene links |
step7TopGenesCaseVsControlExpressionBoxplots |
Create boxplots comparing the expression level of the top genes/transcription factors in case and control samples |
step7TopGenesCircosPlots |
Generate Circos plots displaying the links between top identified genes and each of the RE DNA methylation sites linked to them |
step7TopGenesDNAMethylationHeatmaps |
Generate heatmaps displaying the methylation level of all RE DNA methylation sites linked to the top genes/transcription factors, along with the expression of those genes in the column headers, in the case samples within the supplied MultiAssayExperiment object |
step7TopGenesExpressionCorrelationHeatmaps |
Generate mirrored heatmaps displaying the correlation of the expression values of the top genes/TFs |
step7TopGenesOverlappingLinkedDNAMethylationSitesHeatmaps |
Generate binary heatmaps displaying which of the top genes/transcription factors share links with each of the unique regulatory element DNA methylation sites linked to at least one top gene/TF |
step7TopGenesSurvival |
Perform Kaplan-Meier and Cox regression analyses to assess the association of top gene expression and linked RE DNA methylation site methylation with patient survival |
step7TopGenesTADTables |
Create tables using user-supplied topologically associating domain (TAD) information which identify the topologically associating domains containing each RE DNA methylation site linked to the top genes/transcription factors, as well as other genes in the same topologically associating domain as potential downstream targets |
step7TopGenesUCSCBedFiles |
Create bed-formatted interact files which can be loaded on the UCSC Genome Browser to display links between top genes and transcription factors and their linked RE DNA methylation sites |
step7TopGenesUserPeakOverlap |
Identify if RE DNA methylation sites linked to top genes/transcription factors are located within a specific distance of specified genomic regions |
TCGADownloader |
Download TCGA gene expression, DNA methylation, and clinical datasets and compile them into a MultiAssayExperiment object |
TENETCacheAllData |
Cache all online datasets required by TENET examples and optional features |