RTN-package: 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.

Arguments

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.

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.preprocess:

build associated variant sets for objects of class AVS.

avs.vse:

variant set enrichment analysis.

avs.evse:

an eQTL/VSE pipeline for variant set enrichment analysis.

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.

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

References

Castro, M. A. A. et al. RTN: Reconstruction and Analysis of Transcriptional Networks. Journal Paper (in preparation), 2013.