Reconstruction of transcriptional networks and analysis of master regulators


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Documentation for package ‘RTN’ version 1.6.2

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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.