RTN-package: Reconstruction and Analysis of Transcriptional Networks.

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

Description

A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

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.gsea2:	compute regulon activity.
tni.prune:	prune regulons to remove redundant targets for regulon activity analysis.
tni.sre:	subgroup regulon difference analysis.
tni.plot.sre:	plot subgroup regulon rnrichment .
tni.regulon.summary:	return a summary of network and regulons.
tni.plot.checks:	plot regulon target counts.
tni.alpha.adjust:	adjust the significance level for two datasets.
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.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.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 by typing help.start() and selecting the RTN package from the menu.

Author(s)

Maintainer: Mauro Castro <[e-mail]>

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.

RTN documentation built on Nov. 12, 2020, 2:02 a.m.