clusterDist: clusterDist

In phenoDist: Phenotypic distance measures

Description

Clustering analysis based on a distance matrix.

Usage

clusterDist(x, distMatrix, clusterFun='hclust', ...)

Arguments

x	An imageHTS object.
distMatrix	A pair-wise distance matrix or a dist object.
clusterFun	A character string defining the cluster function.
...	Additional arguments to be passed to the cluster function.

Details

This function performs a clustering analysis based on a pair-wise distance matrix such as generated by PDMBySvmAccuracy.

Value

The return from the cluster function, such as an hclust object returned from the hclust function.

Author(s)

Xian Zhang

See Also

hclust, PDMBySvmAccuracy

Examples

  library('phenoDist')

  ## load the imageHTS object
  load(system.file('kimorph', 'kimorph.rda', package='phenoDist'))
  x@localPath <- file.path(tempdir(), 'kimorph')

  ## load sample phenotypic distance matrix
  load(system.file('kimorph', 'svmAccPDM_Pl1.rda', package='phenoDist'))

  ## phenotypic clustering
  phenoCluster <- clusterDist(x, distMatrix=svmAccPDM_Pl1, clusterFun='hclust', method='ward')

  ## Not run: 
  require('GOstats')
  GOEnrich <- enrichAnalysis(x, cl=cutree(phenoCluster, k=5), terms='GO', annotation='org.Hs.eg.db', pvalueCutoff=0.01, testDirection='over', ontology='BP', conditional=TRUE)
    
## End(Not run)

phenoDist documentation built on May 2, 2018, 4:46 a.m.