IntClust: Integrated Data Analysis via Clustering

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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.

Author
Marijke Van Moerbeke
Date of publication
2016-02-15 07:51:46
Maintainer
Marijke Van Moerbeke <marijkevanmoerbeke@uhasselt.be>
License
GPL-3
Version
0.0.1

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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

Files in this package

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