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ccml (version 1.4.0)

Consensus Clustering for Different Sample Coverage Data

Description

Consensus clustering, also called meta-clustering or cluster ensembles, has been increasingly used in clinical data. Current consensus clustering methods tend to ensemble a number of different clusters from mathematical replicates with similar sample coverage. As the fact of common variety of sample coverage in the real-world data, a new consensus clustering strategy dealing with such biological replicates is required. This is a two-step consensus clustering package, which is used to input multiple predictive labels with different sample coverage (missing labels).

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Version

Install

install.packages('ccml')

Monthly Downloads

21

Version

1.4.0

License

GPL-2

Maintainer

Chuanxing Li

Last Published

August 30th, 2023

Functions in ccml (1.4.0)

example_data

The input data for example
callNCW

Calculate normalized consensus weight(NCW) matrix based on permutation.
spectralClusteringAffinity

Perform spectral clustering algorithms for an affinity matrix, using SNFtool::spectralClustering.
ccml

A two-step consensus clustering inputing multiple predictive labels with different sample coverages (missing labels)
randConsensusMatrix

Calculate consensus weight matrix based on the permuted input label matrix. Internal function used by callNCW
plotCompareCW

Plot of original consensus weights vs. normalized consensus weights grouping by the number of co-appeared percent of clustering(non-missing).