| clusterDist {phenoDist} | R Documentation |
Clustering analysis based on a distance matrix.
clusterDist(x, distMatrix, clusterFun='hclust', ...)
x |
An |
distMatrix |
A pair-wise distance matrix or a |
clusterFun |
A character string defining the cluster function. |
... |
Additional arguments to be passed to the cluster function. |
This function performs a clustering analysis based on a pair-wise distance matrix such as generated by PDMBySvmAccuracy.
The return from the cluster function, such as an hclust object returned from the hclust function.
Xian Zhang
hclust, PDMBySvmAccuracy
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)