RTN: Reconstruction of transcriptional networks and analysis of master regulators
Version 1.14.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorMauro Castro, Xin Wang, Michael Fletcher, Florian Markowetz and Kerstin Meyer
Bioconductor views GeneExpression GeneRegulation GeneSetEnrichment GeneticVariability GraphAndNetwork NetworkEnrichment NetworkInference SNP
Date of publicationNone
MaintainerMauro Castro <mauro.a.castro@gmail.com>
LicenseArtistic-2.0
Version1.14.0
URL http://dx.doi.org/10.1038/ncomms3464
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RTN")

Man pages

AVS-class: Class '"AVS"': an S4 class for variant set enrichment...
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.
avs.preprocess.LD1000gRel20130502: A preprocessing function for objects of class AVS.
avs.preprocess.LDHapMapRel27: A preprocessing function for objects of class AVS.
avs.vse: Variant set enrichment (VSE) analysis.
RTN.data: A pre-processed dataset for the RTN package.
RTN-package: Reconstruction and Analysis of Transcriptional Networks.
TNA-class: Class '"TNA"': an S4 class for Transcriptional Network...
tna.get: Get information from individual slots in a TNA object.
tna.graph: Compute a graph from TNA objects.
tna.gsea1: One-tailed Gene Set Enrichment Analysis (GSEA) over a list of...
tna.gsea2: Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of...
tna.mra: Master Regulator Analysis (MRA) over a list of regulons.
tna.overlap: Overlap analysis over a list of regulons.
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.synergy: Synergy analysis over a list of regulons.
tni2tna.preprocess: A preprocessing function for objects of class TNI.
tni.bootstrap: Inference of consensus transcriptional networks.
TNI-class: Class '"TNI"': an S4 class for Transcriptional Network...
tni.conditional: Modulators of transcription factor (TF) activity assessed by...
tni.dpi.filter: Data Processing Inequality (DPI) filter.
tni.get: Get information from individual slots in a TNI object.
tni.graph: Compute a graph from TNI objects.
tni.gsea2: Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of...
tni.permutation: Inference of transcriptional networks.
tni.preprocess: A preprocessing function for objects of class TNI.

Functions

AVS-class Man page
RTN Man page
RTN-package Man page
TNA-class Man page
TNI-class Man page
avs.checks Source code
avs.evse Man page
avs.evse,AVS-method Man page
avs.get Man page
avs.get,AVS-method Man page
avs.initialize Source code
avs.mapranges Source code
avs.plot1 Man page Source code
avs.plot2 Man page Source code
avs.preprocess.LD1000gRel20130502 Man page Source code
avs.preprocess.LDHapMapRel27 Man page Source code
avs.vse Man page
avs.vse,AVS-method Man page
avsplot1 Source code
avsplot2 Source code
buildAVS.LD1000gRel20130502 Source code
buildAVS.LDHapMapRel27 Source code
buildRandomAVS.LD1000gRel20130502 Source code
buildRandomAVS.LDHapMapRel27 Source code
cdt.get Source code
cdt.getReverse Source code
cdt.stability Source code
check.colinked Source code
check.format1 Source code
check.format2 Source code
checkModuationEffect Source code
checkUniverse.LD1000gRel20130502 Source code
checkUniverse.LDHapMapRel27 Source code
cv.filter Source code
data.integration Source code
drcircle Source code
dt4rtn Man page
eqtlExtract Source code
eqtlExtractAnova Source code
eqtlExtractFull Source code
eqtlTest Source code
eqtlTestDetailed Source code
eqtlTestDetailedAnova Source code
evsea Source code
evseaproxy Source code
get.avsdist Source code
get.eqtldist Source code
get.merged.data1 Source code
get.merged.data2 Source code
getAnnotOverlap Source code
getAnnotRanges Source code
getAvsRanges Source code
getEvseEqtls Source code
getEvseMatrix Source code
getMappedClusters Source code
getMappedMarkers Source code
getMarkers.rset Source code
getMarkers.vset Source code
getRandomAvsRanges Source code
getUniverseCounts1 Source code
getUniverseCounts2 Source code
getldata Source code
gettfs Source code
gsea1tna Source code
gsea2tna Source code
gsea2tni Source code
gseaScores4CMAP Source code
gseaScores4RTN Source code
gseaScoresBatch4RTN Source code
gseaScoresBatchParallel4RTN Source code
gsplot1 Source code
gsplot2 Source code
hcEdges.filter Source code
hclust2igraph Source code Source code
hits.preprocess Source code
hyperGeoTest4RTN Source code
isParallel Source code
make.plot1 Source code
make.plot2 Source code
maprset Source code
mapvset Source code
miMdTfStats Source code
miThresholdMd Source code
miThresholdMdTf Source code
mtdata Source code
multiHyperGeoTest4RTN Source code
p.adjust.cdt Source code
pairwiseShadow Source code
pairwiseSynergy Source code
perm.pmin.pooled Source code
perm.pmin.separate Source code
pheno.preprocess Source code
plot.gsea1 Source code
plot.gsea2 Source code
report.vset Source code
run.gsea1 Source code
run.gsea2 Source code
run.overlap Source code
run.shadow Source code
run.synergy Source code
run.tna.cmap Source code
run.tni.gsea2 Source code
setregs1 Source code
setregs2 Source code
shtest Source code
sortAnnotation Source code
sortPosition Source code
sortblock.cdt Source code
tna.duplicate.remover Source code
tna.get Man page
tna.get,TNA-method Man page
tna.graph Man page
tna.graph,TNA-method Man page
tna.gsea1 Man page
tna.gsea1,TNA-method Man page
tna.gsea2 Man page
tna.gsea2,TNA-method Man page
tna.hyper Source code
tna.hyper.pairs Source code
tna.mra Man page
tna.mra,TNA-method Man page
tna.overlap Man page
tna.overlap,TNA-method Man page
tna.permutation.pvalues Source code
tna.permutation.pvalues.shadow Source code
tna.plot.gsea1 Man page Source code
tna.plot.gsea2 Man page Source code
tna.preprocess Source code
tna.shadow Man page
tna.shadow,TNA-method Man page
tna.synergy Man page
tna.synergy,TNA-method Man page
tnai.checks Source code
tni.amap Source code
tni.boot Source code
tni.bootstrap Man page
tni.bootstrap,TNI-method Man page
tni.conditional Man page
tni.conditional,TNI-method Man page
tni.cor Source code
tni.dpi Source code
tni.dpi.filter Man page
tni.dpi.filter,TNI-method Man page
tni.get Man page
tni.get,TNI-method Man page
tni.graph Man page
tni.graph,TNI-method Man page
tni.gsea2 Man page
tni.gsea2,TNI-method Man page
tni.mmap Source code
tni.mmap.detailed Source code
tni.perm.pooled Source code
tni.perm.separate Source code
tni.permutation Man page
tni.permutation,TNI-method Man page
tni.permutation.pvalues Source code
tni.phyper Source code
tni.pmin Source code
tni.preprocess Man page
tni.preprocess,TNI-method Man page
tni.rmap Source code
tni2tna.preprocess Man page
tni2tna.preprocess,TNI-method Man page
translateQuery Source code
treemap Source code
validateMarkers Source code
validateSnpop Source code
vsea Source code
vseformat Source code
vsereport Source code

Files

DESCRIPTION
NAMESPACE
R
R/AVS-constructors.R
R/AVS-methods.R
R/AllChecks.R
R/AllClasses.R
R/AllGenerics.R
R/AllPlotsAVS.R
R/AllPlotsTNA.R
R/AllSupplementsAVS.R
R/AllSupplementsTNA.R
R/AllSupplementsTNI.R
R/ClassUnions.R
R/TNA-methods.R
R/TNI-methods.R
build
build/vignette.rds
data
data/datalist
data/dt4rtn.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/RTN.R
inst/doc/RTN.Rnw
inst/doc/RTN.pdf
inst/unitTests
inst/unitTests/test_rtn.R
man
man/AVS-class.Rd
man/RTN-package.Rd
man/RTN.data.Rd
man/TNA-class.Rd
man/TNI-class.Rd
man/avs.evse.Rd
man/avs.get.Rd
man/avs.plot1.Rd
man/avs.plot2.Rd
man/avs.preprocess.LD1000gRel20130502.Rd
man/avs.preprocess.LDHapMapRel27.Rd
man/avs.vse.Rd
man/tna.get.Rd
man/tna.graph.Rd
man/tna.gsea1.Rd
man/tna.gsea2.Rd
man/tna.mra.Rd
man/tna.overlap.Rd
man/tna.plot.gsea1.Rd
man/tna.plot.gsea2.Rd
man/tna.shadow.Rd
man/tna.synergy.Rd
man/tni.bootstrap.Rd
man/tni.conditional.Rd
man/tni.dpi.filter.Rd
man/tni.get.Rd
man/tni.graph.Rd
man/tni.gsea2.Rd
man/tni.permutation.Rd
man/tni.preprocess.Rd
man/tni2tna.preprocess.Rd
tests
tests/runTests.R
vignettes
vignettes/RTN.Rnw
vignettes/bib.bib
RTN documentation built on May 20, 2017, 10:08 p.m.