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 |