# RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

## Documentation for package ‘RTN’ version 2.16.0

- 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.
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.