consensus_clustering_scExp: Wrapper to apply ConsensusClusterPlus to scExp object

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Wrapper to apply ConsensusClusterPlus to scExp object

Description

Runs consensus hierarchical clustering on PCA feature space of scExp object. Plot consensus scores for each number of clusters. See ConsensusClusterPlus - Wilkerson, M.D., Hayes, D.N. (2010). ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics, 2010 Jun 15;26(12):1572-3.

Usage

consensus_clustering_scExp(
  scExp,
  prefix = NULL,
  maxK = 10,
  reps = 100,
  pItem = 0.8,
  pFeature = 1,
  distance = "pearson",
  clusterAlg = "hc",
  innerLinkage = "ward.D",
  finalLinkage = "ward.D",
  plot_consclust = "pdf",
  plot_icl = "png"
)

Arguments

scExp	A SingleCellExperiment object containing 'PCA' in reducedDims.
prefix	character value for output directory. Directory is created only if plot_consclust is not NULL. This title can be an abosulte or relative path.
maxK	integer value. maximum cluster number to evaluate. (10)
reps	integer value. number of subsamples. (100)
pItem	numerical value. proportion of items to sample. (0.8)
pFeature	numerical value. proportion of features to sample. (1)
distance	character value. 'pearson': (1 - Pearson correlation), 'spearman' (1 - Spearman correlation), 'euclidean', 'binary', 'maximum', 'canberra', 'minkowski' or custom distance function. ('pearson')
clusterAlg	character value. cluster algorithm. 'hc' heirarchical (hclust), 'pam' for paritioning around medoids, 'km' for k-means upon data matrix, 'kmdist' ('hc') for k-means upon distance matrices (former km option), or a function that returns a clustering. ('hc')
innerLinkage	hierarchical linkage method for subsampling. ('ward.D')
finalLinkage	hierarchical linkage method for consensus matrix. ('ward.D')
plot_consclust	character value. NULL - print to screen, 'pdf', 'png', 'pngBMP' for bitmap png, helpful for large datasets. ('pdf')
plot_icl	same as above for item consensus plot. ('png')

Details

This functions takes as input a SingleCellExperiment object that must have 'PCA' in reducedDims and outputs a SingleCellExperiment object containing consclust list calculated cluster consensus and item consensus scores in metadata.

Value

Returns a SingleCellExperiment object containing consclust list, calculated cluster consensus and item consensus scores in metadata.

References

ConsensusClusterPlus package by Wilkerson, M.D., Hayes, D.N. (2010). ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics, 2010 Jun 15;26(12):1572-3.

Examples

data("scExp")
scExp_cf = correlation_and_hierarchical_clust_scExp(scExp)
scExp_cf = consensus_clustering_scExp(scExp)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.