GetClustering: Get 'Benchmark' clustering result

In davnovak/SingleBench: Framework for benchmarking and optimising dimension-reduction and clustering pipelines in expression data analysis

Description

Extracts the result of a clustering tool that is part of a benchmark sub-pipeline that was set up previously. If stability analysis is turned on for the benchmark, either results of all runs of the clustering can be returned, or only the result of a single run on the full expression data can be returned.

Usage

GetClustering(
  benchmark,
  idx.subpipeline,
  idx.n_param = NULL,
  all_runs = FALSE,
  concatenate = TRUE
)

Arguments

benchmark	object of type Benchmark
idx.subpipeline	integer: index of a sub-pipeline of benchmark
idx.n_param	integer: index of an n-parameter iteration of a sub-pipeline of benchmark
all_runs	logical: whether results of all runs should be returned (in a list). Default value is FALSE

Details

If you choose to extract results of all runs of a clustering algorithm which clustered on bootstraps of the original data, the last slot in the list contains the single run on original data. Furthermore, you can extract bootstrap indices using GetBootstrapIndices.

See Also

• Benchmark: constructs a Benchmark object (benchmark pipeline set-up)\

• Evaluate: runs all benchmark sub-pipelines and scores the performance of each tool

davnovak/SingleBench documentation built on Dec. 19, 2021, 9:10 p.m.