IntClust: Integrated Data Analysis via Clustering
Version 0.0.1

Several integrative data methods in which information of objects from different data sources can be combined are included in the IntClust package. As a single data source is limited in its point of view, this provides more insight and the opportunity to investigate how the variables are interconnected. Clustering techniques are to be applied to the combined information. For now, only agglomerative hierarchical clustering is implemented. Further, differential gene expression and pathway analysis can be conducted on the clusters. Plotting functions are available to visualize and compare results of the different methods.

AuthorMarijke Van Moerbeke
Date of publication2016-02-15 07:51:46
MaintainerMarijke Van Moerbeke <marijkevanmoerbeke@uhasselt.be>
LicenseGPL-3
Version0.0.1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("IntClust", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

ADC: Aggregated Data Clustering
ADECa: Aggregated Data Ensemble Clustering - version a
ADECc: Aggregated Data Ensemble Clustering - version c
BoxPlotDistance: Box plots of one distance matrix categorized against another...
IntClust-package: Integrated Data Analysis
SNFa: Similarity Network Fusion - version a
SNFc: Similarity Network Fusion - version c
See all...

All man pages Function index File listing

Man pages

ADC: Aggregated Data Clustering
ADEC: Aggregated Data Ensemble Clustering
ADECa: Aggregated Data Ensemble Clustering - version a
ADECb: Aggregated Data Ensemble Clustering - version b
ADECc: Aggregated Data Ensemble Clustering - version c
BinFeaturesPlot: Plot of a selection of features
BoxPlotDistance: Box plots of one distance matrix categorized against another...
CEC: Complementary Ensemble Clustering
CECa: Complementary Ensemble Clustering - version a
CECb: Complementary Ensemble Clustering - version b
CECc: Complementary Ensemble Clustering - version c
CharacteristicFeatures: Determining the characteristic features of a cluster
ChooseCluster: Interactive plot to determine DE Genes and DE features for a...
Cluster: Perform clustering on a single data source
ClusterPlot: Plot a dendrogram with leaves colored by a result of choice
Colorpalette: Create a color palette to be used in the plots
Colors1: First example for colors
Colors2: Second example for colors
ColorsNames: Function that annotates colors to their names
CompareInteractive: Interactive comparison of clustering results for a specific...
ComparePlot: Comparison of clustering results over multiple results
CompareSilCluster: Compares medoid clustering results based on silhouette widths
CompareSvsM: Comparison of clustering results for the single and multiple...
ContFeaturesPlot: Plot of continuous features
DetermineWeight_SilClust: Determines an optimal weight for weighted clustering by...
DetermineWeight._SimClust: Determines an optimal weight for weighted clustering by...
DiffGenes: Differential gene expressions for multiple results
Distance: Distance function
FeaturesOfCluster: Lists all features present in a selected cluster of compounds
FindCluster: Find a selection of compounds in the output of...
FindElement: Find an element in a data structure
FindGenes: Investigates whether genes are differential expressed in...
fingerprintMat: The fingerprint matrix for the MCF7 data
GeneInfo: The gene info data frame
geneMat: The gene expression matrix
Geneset.intersect: Intersection over resulting gene sets of 'PathwaysIter'...
GS: List of GO Annotations
HeatmapPlot: Comparing two clustering results with a heatmap
HeatmapSelection: A function to select a group of compounds via the similarity...
IntClust-package: Integrated Data Analysis
LabelPlot: Coloring specific leaves of a dendrogram
Normalization: A normalization function
PathwayAnalysis: Pathway Analysis
Pathways: Pathway analysis for multiple clustering results
PathwaysIter: Iterations of the pathway analysis
PlotPathways: A GO plot of a pathway analysis output.
PreparePathway: Preparing a data set for pathway analysis
ProfilePlot: Plotting gene profiles
ReorderToReference: Order the outputs of the clustering methods against a...
SelectnrClusters: Determines an optimal number of clusters based on silhouette...
SharedComps: Intersection of clusters over multiple methods
SharedGenesPathsFeat: Intersection of genes and pathways over multiple methods
SimilarityHeatmap: A heatmap of similarity values between compounds
SimilarityMeasure: A measure of similarity for the outputs of the different...
SNF: Similarity Network Fusion
SNFa: Similarity Network Fusion - version a
SNFb: Similarity Network Fusion - version b
SNFc: Similarity Network Fusion - version c
targetMat: The target prediction matrix
TrackCluster: Follow a cluster over multiple methods
Ultimate: Function that performs any aggregated data function
WeightedClust: Weighted clustering
WeightedSimClust: Weighted similarity clustering
WonM: Weighting on Membership

Functions

ADC Man page Source code
ADEC Man page Source code
ADECa Man page Source code
ADECb Man page Source code
ADECc Man page Source code
BinFeaturesPlot Man page Source code
BoxPlotDistance Man page Source code
CEC Man page Source code
CECa Man page Source code
CECb Man page Source code
CECc Man page Source code
CharacteristicFeatures Man page Source code
ChooseCluster Man page Source code
Cluster Man page Source code
ClusterCols Source code
ClusterPlot Man page Source code
ColorPalette Man page Source code
Colors1 Man page
Colors2 Man page
ColorsNames Man page Source code
CompareInteractive Man page Source code
ComparePlot Man page Source code
CompareSilCluster Man page Source code
CompareSvsM Man page Source code
ContFeaturesPlot Man page Source code
DetermineWeight_SilClust Man page Source code
DetermineWeight_SimClust Man page Source code
DiffGenes Man page Source code
DiffGenesSelection Source code
Distance Man page Source code
FeatSelection Source code
FeaturesOfCluster Man page Source code
FindCluster Man page Source code
FindElement Man page Source code
FindGenes Man page Source code
GS Man page
GeneInfo Man page
Geneset.intersect Man page Source code
Geneset.intersectSelection Source code
HeatmapPlot Man page Source code
HeatmapSelection Man page Source code
IntClust-package Man page
LabelCols Source code
LabelPlot Man page Source code
Normalization Man page Source code
PathwayAnalysis Man page Source code
Pathways Man page Source code
PathwaysIter Man page Source code
PathwaysSelection Source code
PlotPathways Man page Source code
PreparePathway Man page Source code
ProfilePlot Man page Source code
ReorderToReference Man page Source code
SNF Man page Source code
SNFa Man page Source code
SNFb Man page Source code
SNFc Man page Source code
SelectnrClusters Man page Source code
SharedComps Man page Source code
SharedGenesPathsFeat Man page Source code
SharedSelection Source code
SharedSelectionLimma Source code
SharedSelectionMLP Source code
SimilarityHeatmap Man page Source code
SimilarityMeasure Man page Source code
TrackCluster Man page Source code
Ultimate Man page Source code
WeightedClust Man page Source code
WeightedSimClust Man page Source code
WonM Man page Source code
distanceheatmaps Source code
fingerprintMat Man page
geneMat Man page
targetMat Man page

Files

DESCRIPTION
NAMESPACE
R
R/ADC.R
R/ADEC.R
R/ADECa.R
R/ADECb.R
R/ADECc.R
R/BinFeaturesPlot.R
R/BoxPlotDistance.R
R/CEC.R
R/CECa.R
R/CECb.R
R/CECc.R
R/CharacteristicsFeatures.R
R/ChooseCluster.R
R/Cluster.R
R/ClusterCols.R
R/Clusterplot.R
R/Colorpalette.R
R/ColorsNames.R
R/CompareInteractive.R
R/ComparePlot.R
R/CompareSilCluster.R
R/CompareSvsM.R
R/ContFeaturesPlot.R
R/DetermineWeight_SilClust.R
R/DetermineWeight_SimClust.R
R/DiffGenes.R
R/DiffGenesSelection.R
R/Distance.R
R/FeatSelection.R
R/FeaturesOfCluster.R
R/FindCluster.R
R/FindElement.R
R/FindGenes.R
R/Geneset.intersect.R
R/Geneset.intersectSelection.R
R/HeatmapPlot.R
R/HeatmapSelection.R
R/IntClust-internal.R
R/LabelCols.R
R/Labelplot.R
R/Normalization.R
R/PathwayAnalysis.R
R/Pathways.R
R/PathwaysIter.R
R/PathwaysSelection.R
R/PlotPathways.R
R/PreparePathway.R
R/ProfilePlot.R
R/ReorderToReference.R
R/SNF.R
R/SNFa.R
R/SNFb.R
R/SNFc.R
R/SelectnrClusters.R
R/SharedComps.R
R/SharedGenesPathsFeat.R
R/SharedSelection.R
R/SharedSelectionLimma.R
R/SharedSelectionMLP.R
R/SimilarityHeatmap.R
R/SimilarityMeasure.R
R/TrackCluster.R
R/Ultimate.R
R/WeightedClust.R
R/WeightedSimClust.R
R/WonM.R
R/distanceheatmaps.R
build
build/vignette.rds
data
data/Colors1.RData
data/Colors2.RData
data/GS.RData
data/GeneInfo.rda
data/datalist
data/fingerprintMat.rda
data/geneMat.rda
data/targetMat.rda
inst
inst/doc
inst/doc/IntClustVignette.R
inst/doc/IntClustVignette.Rnw
inst/doc/IntClustVignette.pdf
man
man/ADC.Rd
man/ADEC.Rd
man/ADECa.Rd
man/ADECb.Rd
man/ADECc.Rd
man/BinFeaturesPlot.Rd
man/BoxPlotDistance.Rd
man/CEC.Rd
man/CECa.Rd
man/CECb.Rd
man/CECc.Rd
man/CharacteristicFeatures.Rd
man/ChooseCluster.Rd
man/Cluster.Rd
man/ClusterPlot.Rd
man/Colorpalette.Rd
man/Colors1.Rd
man/Colors2.Rd
man/ColorsNames.Rd
man/CompareInteractive.Rd
man/ComparePlot.Rd
man/CompareSilCluster.Rd
man/CompareSvsM.Rd
man/ContFeaturesPlot.Rd
man/DetermineWeight._SimClust.Rd
man/DetermineWeight_SilClust.Rd
man/DiffGenes.Rd
man/Distance.Rd
man/FeaturesOfCluster.Rd
man/FindCluster.Rd
man/FindElement.Rd
man/FindGenes.Rd
man/GS.Rd
man/GeneInfo.Rd
man/Geneset.intersect.Rd
man/HeatmapPlot.Rd
man/HeatmapSelection.Rd
man/IntClust-package.Rd
man/LabelPlot.Rd
man/Normalization.Rd
man/PathwayAnalysis.Rd
man/Pathways.Rd
man/PathwaysIter.Rd
man/PlotPathways.Rd
man/PreparePathway.Rd
man/ProfilePlot.Rd
man/ReorderToReference.Rd
man/SNF.Rd
man/SNFa.Rd
man/SNFb.Rd
man/SNFc.Rd
man/SelectnrClusters.Rd
man/SharedComps.Rd
man/SharedGenesPathsFeat.Rd
man/SimilarityHeatmap.Rd
man/SimilarityMeasure.Rd
man/TrackCluster.Rd
man/Ultimate.Rd
man/WeightedClust.Rd
man/WeightedSimClust.Rd
man/WonM.Rd
man/fingerprintMat.Rd
man/geneMat.Rd
man/targetMat.Rd
vignettes
vignettes/BVSPermbib.bib
vignettes/CompareSvsM.pdf
vignettes/HeatmapSelection_MCF7W.pdf
vignettes/IntClustVignette-ComparePlot.pdf
vignettes/IntClustVignette-CompareSvsM.pdf
vignettes/IntClustVignette-FeaturesPlotF.pdf
vignettes/IntClustVignette-FeaturesPlotFP.pdf
vignettes/IntClustVignette-FeaturesPlotT.pdf
vignettes/IntClustVignette.Rnw
vignettes/Interactive.png
vignettes/Interactive1.pdf
vignettes/InteractiveCluster.pdf
vignettes/InteractiveMethod.pdf
vignettes/SimilarityHeatmap_MCF7W.pdf
vignettes/Tracking.pdf
vignettes/asa.bst
IntClust documentation built on May 21, 2017, 1:20 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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