RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

---

Documentation for package ‘RTN’ version 2.30.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

RTN-package	Reconstruction and Analysis of Transcriptional Networks.
AVS-class	Class '"AVS"': an S4 class for variant set enrichment analysis.
avs.evse	An eQTL/VSE pipeline for variant set enrichment analysis.
avs.evse-method	Class '"AVS"': an S4 class for variant set enrichment analysis.
avs.get	Get information from individual slots in an AVS object.
avs.get-method	Class '"AVS"': an S4 class for variant set enrichment analysis.
avs.pevse	An EVSE pipeline using precomputed eQTLs.
avs.pevse-method	Class '"AVS"': an S4 class for variant set enrichment analysis.
avs.plot1	Plot results from AVS methods, single plots.
avs.plot2	Plot results from AVS methods, multiple plots.
avs.rvse	An rQTL/VSE pipeline for variant set enrichment analysis.
avs.rvse-method	Class '"AVS"': an S4 class for variant set enrichment analysis.
avs.vse	Variant set enrichment (VSE) analysis.
avs.vse-method	Class '"AVS"': an S4 class for variant set enrichment analysis.
pksData	Pre-processed datasets for the RTN package.
RTN	Reconstruction and Analysis of Transcriptional Networks.
stni	A pre-processed TNI for demonstration purposes only.
tfsData	Pre-processed datasets for the RTN package.
TNA-class	Class '"TNA"': an S4 class for Transcriptional Network Analysis.
tna.get	Get information from individual slots in a TNA object.
tna.get-method	Class '"TNA"': an S4 class for Transcriptional Network Analysis.
tna.gsea1	One-tailed Gene Set Enrichment Analysis (GSEA) over a list of regulons.
tna.gsea1-method	Class '"TNA"': an S4 class for Transcriptional Network Analysis.
tna.gsea2	Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of regulons.
tna.gsea2-method	Class '"TNA"': an S4 class for Transcriptional Network Analysis.
tna.mra	Master Regulator Analysis (MRA) over a list of regulons.
tna.mra-method	Class '"TNA"': an S4 class for Transcriptional Network Analysis.
tna.plot.gsea1	Plot enrichment analyses from TNA objects.
tna.plot.gsea2	Plot enrichment analyses from TNA objects.
tnaData	Pre-processed datasets for the RTN package.
TNI-class	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.alpha.adjust	Adjust the significance level for two datasets.
tni.annotate.regulons	Annotate regulons with external gene set collections.
tni.annotate.regulons-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.annotate.samples	Annotate samples with external gene set collections.
tni.annotate.samples-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.area3	Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm
tni.area3-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.bootstrap	Inference of consensus transcriptional networks.
tni.bootstrap-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.conditional	Modulators of transcription factor (TF) activity assessed by conditional mutual information analysis.
tni.conditional-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.constructor	A constructor for objects of class TNI.
tni.dpi.filter	Data Processing Inequality (DPI) filter.
tni.dpi.filter-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.get	Get information from individual slots in a TNI object.
tni.get-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.graph	Compute a graph from TNI objects (Deprecated).
tni.graph-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.gsea2	Compute regulon activity by calling GSEA2 (two-tailed Gene Set Enrichment Analysis) algorithm
tni.gsea2-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.overlap.genesets	Associate regulons with external gene set collections.
tni.overlap.genesets-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.permutation	Inference of transcriptional networks.
tni.permutation-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.plot.checks	Plot regulon target counts.
tni.plot.sre	Plot Subgroup Regulon Enrichment for TNI-class objects.
tni.preprocess	A preprocessing function for objects of class TNI.
tni.preprocess-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.prune	Prune regulons to remove redundant targets for regulon activity analysis
tni.prune-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.regulon.summary	Summary of regulon characteristics.
tni.regulon.summary-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.replace.samples	Entry point to assess new samples with previously calculated regulons.
tni.replace.samples-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.sre	Subgroup Regulon Enrichment for TNI-class objects.
tni.sre-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni2tna.preprocess	A preprocessing function for objects of class TNI.
tni2tna.preprocess-method	Class '"TNI"': an S4 class for Transcriptional Network Inference.
tniData	Pre-processed datasets for the RTN package.
upgradeTNA	Upgrade objects of class TNI.
upgradeTNI	Upgrade objects of class TNI.