The polyClustR package provides an R implementation of the pipeline described in polyCluster: Defining Communities of Reconciled Cancer Subtypes with Biological and Prognostic Significance; K. Eason, G. Nyamundanda and A. Sadandandam.
devtools::install_github('syspremed/polyClustR')
library(polyClustR)
# Example breast dataset is provided with installation
exampleGE <- system.file('extdata', 'chin_breast_example_GE.txt', package = 'polyClustR')
exampleKnownSubtypes <- system.file('extdata', 'chin_breast_example_known_subtypes.txt', package = 'polyClustR')
polyCluster(exampleGE, clusterAlg = c('hc', 'km'), phenoFile = exampleKnownSubtypes, ref = 'test_run')
# Output is written to the current working directory.For full details of the arguments required to run polyCluster, see ?polyCluster.
If you have any issues running polyClustR, please report them using the "Issues" tab above.
Default clustering parameters are:
| Parameter | Value |
|---|---|
| Consensus resamplings | 100 |
| Proportion of items sampled per subsample | 0.8 |
| Clustering distance | Euclidean (km), Pearson (hc) |
| Heirarchical linkage method for subsampling | Average |
| Heirarchical linkage method for consensus matrix | Average |