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Change biological functional annotation from list to TRUE / FALSE matrix
● Data Source:
CranContrib
● Keywords: cluster
● Alias: annotationListToMatrix
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plot.sota
(Package: clValid) :
Plot Function for a SOTA Object
'plot.sota' is used to obtain a visual representation of profiles within each individual cluster. Corresponding cluster average profiles are also available. By default, plots for all clusters are displayed side by side.
● Data Source:
CranContrib
● Keywords: cluster, hplot
● Alias: plot.sota
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The class "clValid" contains the clustering results and validation measures from the accompanying call to the function clValid.
● Data Source:
CranContrib
● Keywords: classes, cluster
● Alias: clValid-class, clValidObj
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BSI
(Package: clValid) :
Biological Stability Index
Calculates the biological stability index (BSI) for a given statistical clustering partition and biological annotation.
● Data Source:
CranContrib
● Keywords: cluster
● Alias: BSI
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sota
(Package: clValid) :
Self-organizing Tree Algorithm (SOTA)
Computes a Self-organizing Tree Algorithm (SOTA) clustering of a dataset returning a SOTA object.
● Data Source:
CranContrib
● Keywords: cluster
● Alias: sota
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getRanksWeights
(Package: clValid) :
Extract ranks and weights from clValid object
Creates matrix of ranks and weights from clValid object, to use as input for rank aggregation using RankAggreg in package RankAggreg
● Data Source:
CranContrib
● Keywords: cluster
● Alias: getRanksWeights
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BHI
(Package: clValid) :
Biological Homogeneity Index
Calculates the biological homogeneity index (BHI) for a given statistical clustering partition and biological annotation.
● Data Source:
CranContrib
● Keywords: cluster
● Alias: BHI
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Calculates the connectivity validation measure for a given cluster partitioning.
● Data Source:
CranContrib
● Keywords: cluster
● Alias: connectivity
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clValid
(Package: clValid) :
Validate Cluster Results
clValid reports validation measures for clustering results. The function returns an object of class "clValid", which contains the clustering results in addition to the validation measures. The validation measures fall into three general categories: "internal", "stability", and "biological".
● Data Source:
CranContrib
● Keywords: cluster
● Alias: clValid
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This function reads in a biological annotation file detailing the functional classes for a given set of genes from a comma separated file.
● Data Source:
CranContrib
● Keywords: cluster
● Alias: readAnnotationFile
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providing 
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