Man pages for RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

AVS-classClass '"AVS"': an S4 class for variant set enrichment...
avs.evseAn eQTL/VSE pipeline for variant set enrichment analysis.
avs.getGet information from individual slots in an AVS object.
avs.pevseAn EVSE pipeline using precomputed eQTLs.
avs.plot1Plot results from AVS methods, single plots.
avs.plot2Plot results from AVS methods, multiple plots.
avs.vseVariant set enrichment (VSE) analysis.
RTN.dataPre-processed datasets for the RTN package.
RTN-packageReconstruction and Analysis of Transcriptional Networks.
TNA-classClass '"TNA"': an S4 class for Transcriptional Network...
tna.getGet information from individual slots in a TNA object.
tna.gsea1One-tailed Gene Set Enrichment Analysis (GSEA) over a list of...
tna.gsea2Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of...
tna.mraMaster Regulator Analysis (MRA) over a list of regulons.
tna.plot.gsea1Plot enrichment analyses from TNA objects.
tna.plot.gsea2Plot enrichment analyses from TNA objects.
tni2tna.preprocessA preprocessing function for objects of class TNI.
tni.alpha.adjustAdjust the significance level for two datasets.
tni.annotate.regulonsAnnotate regulons with external gene set collections.
tni.annotate.samplesAnnotate samples with external gene set collections.
tni.area3Compute regulon activity by calling aREA (analytic Rank-based...
tni.bootstrapInference of consensus transcriptional networks.
TNI-classClass '"TNI"': an S4 class for Transcriptional Network...
tni.conditionalModulators of transcription factor (TF) activity assessed by...
tni.constructorA constructor for objects of class TNI.
TNI.dataA pre-processed TNI for demonstration purposes only.
tni.dpi.filterData Processing Inequality (DPI) filter.
tni.getGet information from individual slots in a TNI object.
tni.graphCompute a graph from TNI objects.
tni.gsea2Compute regulon activity by calling GSEA2 (two-tailed Gene...
tni.overlap.genesetsAssociate regulons with external gene set collections.
tni.permutationInference of transcriptional networks.
tni.plot.checksPlot regulon target counts.
tni.plot.srePlot Subgroup Regulon Enrichment for TNI-class objects.
tni.preprocessA preprocessing function for objects of class TNI.
tni.prunePrune regulons to remove redundant targets for regulon...
tni.regulon.summarySummary of regulon characteristics.
tni.replace.samplesEntry point to assess new samples with previously calculated...
tni.sreSubgroup Regulon Enrichment for TNI-class objects.
upgradeTNAUpgrade objects of class TNI.
upgradeTNIUpgrade objects of class TNI.
RTN documentation built on Nov. 12, 2020, 2:02 a.m.