RTN-package {RTN} | R Documentation

## Reconstruction and Analysis of Transcriptional Networks.

### Description

This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.

### Details

Package: | RTN
Type: | Package
Depends: | R (>= 2.15), methods, igraph
Imports: | RedeR, minet, snow, limma, data.table, ff, car, IRanges
Suggests: | HTSanalyzeR, RUnit, BiocGenerics
License: | Artistic-2.0
biocViews: | NetworkInference, GeneRegulation, GeneExpression, GraphsAndNetworks
Collate: | ClassUnions.R, AllChecks.R, AllClasses.R, AllGenerics.R, AllSupplements.R, AllPlots.R, TNA-methods.R, TNI-methods.R,AVS-methods.R
LazyLoad: | yes

### Index

TNI-class: | an S4 class for Transcriptional Network Inference.
tni.preprocess: | a preprocessing method for objects of class TNI.
tni.permutation: | inference of transcriptional networks.
tni.bootstrap: | inference of transcriptional networks.
tni.dpi.filter: | data processing inequality (DPI) filter.
tni.conditional: | conditional mutual information analysis.
tni.get: | get information from individual slots in a TNI object.
tni.graph: | compute a graph from TNI objects.
tni.regulon.summary: | return a summary of network and regulons.
tni.replace.samples: | replace samples of an existing TNI-class objects.
tni2tna.preprocess: | a preprocessing method for objects of class TNI.
TNA-class: | an S4 class for Transcriptional Network Analysis.
tna.mra: | master regulator analysis (MRA) over a list of regulons.
tna.overlap: | overlap analysis over a list of regulons.
tna.gsea1: | one-tailed gene set enrichment analysis (GSEA) over a list of regulons.
tna.gsea2: | two-tailed gene set enrichment analysis (GSEA) over a list of regulons.
tna.synergy: | synergy analysis over a list of regulons.
tna.shadow: | shadow analysis over a list of regulons.
tna.get: | get information from individual slots in a TNA object.
tna.plot.gsea1: | plot results from the one-tailed GSEA.
tna.plot.gsea2: | plot results from the two-tailed GSEA.
AVS-class: | an S4 class to do enrichment analyses in associated variant sets (AVSs).
avs.vse: | variant set enrichment analysis.
avs.evse: | an eQTL/VSE pipeline for variant set enrichment analysis.
avs.pevse: | an EVSE pipeline using precomputed eQTLs.
avs.get: | get information from individual slots in an AVS object.
avs.plot1: | plot results from AVS methods, single plots.
avs.plot2: | plot results from AVS methods, multiple plots.

Further information is available in the vignettes by typing `vignette("RTN")`. Documented topics are also available in HTML by typing `help.start()` and selecting the RTN package from the menu.

### Author(s)

Maintainer: Mauro Castro <mauro.a.castro@gmail.com>

### References

Fletcher M.N.C. et al., Master regulators of FGFR2 signalling and breast cancer risk. Nature Communications, 4:2464, 2013.

Castro M.A.A. et al., Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, 48:12-21, 2016.

[Package RTN version 2.10.1 Index]