SetRank: Advanced Gene Set Enrichment Analysis
Version 1.1.0

Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments.

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AuthorCedric Simillion
Date of publication2016-05-11 12:06:23
MaintainerCedric Simillion <cedric.simillion@dkf.unibe.ch>
LicenseGPL-3
Version1.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SetRank")

Man pages

buildSetCollection: Create a gene set collection
createCytoscapeVizMap: Create a Cytoscape visual style for one or more SetRank...
createIDConverter: Create a function to convert gene or protein IDs
createPathwayTable: Creates a table of all significant pathways in different...
cytoscapeExport: Prepare networks for visualization in Cytoscape
exportGeneNets: Create gene interaction networks for all significant gene...
exportMultipleResults: Export multiple SetRank networks and accompanying tables.
exportSingleResult: Export a SetRank network and accompanying tables.
fixGraphML: Fix the igraph graphML export
generateContinuousMapping: Generates a continuous VizMap property mapping.
generatePMapping: Generates a visual property mapping for p-value attributes
membershipTable: Create a gene set membership table.
propertyFunctions: Attribute handlers for generating the VizMap XML
setRankAnalysis: Advanced gene set enrichment analysis.
styleXML: VizMap XML template

Functions

as.RankedTestSet Source code
as.UnrankedTestSet Source code
boolJaccard Source code
buildEdgeTable Source code
buildSetCollection Man page Source code
buildSetNet Source code
calculateSetRank Source code
createCytoscapeVizMap Man page Source code
createGeneNetVizFile Source code
createIDConverter Man page Source code
createPathwayTable Man page Source code
createSet Source code
cytoscapeExport Man page Source code
expandWithTermOffspring Source code
exportGeneNets Man page Source code
exportMultipleResults Man page Source code
exportSingleResult Man page Source code
fisherCriticalValues Source code
fisherPValue Source code
fixGraphML Man page Source code
generateContinuousMapping Man page Source code
generatePMapping Man page Source code
getAdjustedPValues Source code
getConditionOrder Source code
getCorrectedPValues Source code
getIntersectionPValue Source code
getLogFCTable Source code
getMaxP Source code
getMissingNodes Source code
getNodeTable Source code
getNodesToDelete Source code
getPValueTable Source code
getPrimarySetPValues Source code
getSetPValue Source code
getSetPValue.RankedTestSet Source code
getSetPValue.UnrankedTestSet Source code
getSetPairStatistics Source code
getSetPairStatistics.RankedTestSet Source code
getSetPairStatistics.UnrankedTestSet Source code
getSetPairStatistics_base Source code
getSignificantIntersections Source code
handleProperty Source code
intersectionTest Source code
jaccardDistanceMatrix Source code
membershipTable Man page Source code
minimalI Source code
orderTable Source code
pAdjustAndCorrect Source code
pack Source code
propertyFunctions Man page
setGlobalAttributes Source code
setRankAnalysis Man page Source code
setRankPValue Source code
sinkDelete Source code
sinkDeletePValue Source code
styleXML Man page
uniqueCount Source code
unpack Source code
writeGeneSetNetwork Source code
writeMembership Source code

Files

inst
inst/extdata
inst/extdata/gene_net_style_template.xml
inst/doc
inst/doc/vignette.pdf
inst/doc/vignette.ltx
NAMESPACE
R
R/set_operators.R
R/createCytoscapeVizMap.R
R/analysis.R
R/sysdata.rda
R/buildSets.R
R/gene_nets.R
R/tables.R
vignettes
vignettes/p-value_correction.png
vignettes/vignette.ltx
MD5
build
build/vignette.rds
DESCRIPTION
man
man/generatePMapping.Rd
man/exportMultipleResults.Rd
man/createIDConverter.Rd
man/fixGraphML.Rd
man/createPathwayTable.Rd
man/cytoscapeExport.Rd
man/styleXML.Rd
man/createCytoscapeVizMap.Rd
man/exportGeneNets.Rd
man/setRankAnalysis.Rd
man/generateContinuousMapping.Rd
man/propertyFunctions.Rd
man/buildSetCollection.Rd
man/membershipTable.Rd
man/exportSingleResult.Rd
SetRank documentation built on May 19, 2017, 9:23 a.m.