clusterDist {phenoDist} | R Documentation

## clusterDist

### 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)

[Package phenoDist version 1.27.0 Index]