runAllIterations: The runAllIterations function

Description Usage Arguments Value

Description

Internal. Runs all the iterations of consensus clustering.

Usage

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runAllIterations(dataMatrix, K, nIters, propSamples, clusterAlgorithm,
  pathOutput, verbose, seed)

Arguments

dataMatrix

matrix or data frame with data to cluster, samples/items in the columns and features in the rows.

K

vector of integers representing numbeer of clusters to evaluate. It can be of length 1 and it does not need to consist of consecutive integers. For example, either of K = 4, K = 2:5 or K = c(5, 10, 15) would work.

nIters

number of iterations (bootstrap samples).

propSamples

proportion of items to sample in each bootstrap sample.

clusterAlgorithm

algorithm to perform the clustering, for the moment only K-means is available.

pathOutput

directory for output files and iterations progress report, the current working directory by default.

verbose

logical, print progress messages to screen. During the bootstrap iterations, a report to monitor the progress is created in pathOutput.

seed

numerical value to set random seed for reproducible results. It uses doRNG package to guarantee reproducible results even when running in parallel.

Value

Vector with consensus index for each pair of samples.


mpru/ConsensusClustering documentation built on May 9, 2019, 5:54 a.m.