# Reconstruction of transcriptional networks and analysis of master regulators

## Documentation for package ‘RTN’ version 1.12.0

- 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.plot1 | Plot results from AVS methods, single plots.
avs.plot2 | Plot results from AVS methods, multiple plots.
avs.preprocess | A preprocessing function for objects of class AVS.
avs.preprocess-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.
dt4rtn | A pre-processed dataset for the RTN package.
RTN | Reconstruction and Analysis of Transcriptional Networks.
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.graph | Compute a graph from TNA objects.
tna.graph-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.overlap | Overlap analysis over a list of regulons.
tna.overlap-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.
tna.shadow | shadow analysis over a list of regulons.
tna.shadow-method | Class '"TNA"': an S4 class for Transcriptional Network Analysis.
tna.synergy | Synergy analysis over a list of regulons.
tna.synergy-method | Class '"TNA"': an S4 class for Transcriptional Network Analysis.
TNI-class | Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.bootstrap | Inference of 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.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.permutation | Inference of transcriptional networks.
tni.permutation-method | Class '"TNI"': an S4 class for Transcriptional Network Inference.
tni.preprocess | A preprocessing function for objects of class TNI.
tni.preprocess-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.