# Integrated Data Analysis via Clustering

## Documentation for package ‘IntClust’ version 0.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

IntClust-package | Integrated Data Analysis
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 distance matrix.
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 specific cluster
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 cluster or method.
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 source clustering.
ContFeaturesPlot | Plot of continuous features
DetermineWeight_SilClust | Determines an optimal weight for weighted clustering by silhouettes widths.
DetermineWeight_SimClust | Determines an optimal weight for weighted clustering by similarity weighted clustering.
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 'ReorderToReference'
FindElement | Find an element in a data structure
FindGenes | Investigates whether genes are differential expressed in multiple clusters
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' function
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 heatmap.
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 reference
SelectnrClusters | Determines an optimal number of clusters based on silhouette widths
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 methods
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