Integrated Data Analysis via Clustering


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Documentation for package ‘IntClust’ version 0.0.2

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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