In syspremed/polyClustR: polyClustR: A pipeline to reconcile clustering solutions

knitr::opts_chunk$set(echo = TRUE)

Introduction

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.

Installation & Usage

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 Heirarchical linkage method for subsampling | Average Heirarchical linkage method for consensus matrix | Average

syspremed/polyClustR documentation built on May 31, 2019, 12:49 a.m.