runKM: Perform Consensus K-Means Clustering

In khazum/ccImpute: ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

Perform Consensus K-Means Clustering

Description

Executes k-means clustering on multiple subsets of data defined by singular value decomposition (SVD) components, and then aggregates the results into a consensus matrix.

Usage

runKM(
  logX,
  v,
  maxSets = 8,
  k,
  consMin = 0.75,
  kmNStart,
  kmMax = 1000,
  BPPARAM = bpparam()
)

Arguments

logX	A (sparse or dense) numeric matrix representing the transpose of a log-normalized gene expression matrix. Rows correspond to cells, and columns correspond to genes.
v	A matrix of right singular vectors obtained from SVD of a distance matrix derived from 'logX'.
maxSets	(Optional) The maximum number of sub-datasets used for consensus clustering (default: 8).
k	(Optional) The number of clusters (cell groups) in the data. If not provided, it is estimated using the Tracy-Widom Bound.
consMin	(Optional) The low-pass filter threshold for processing the consensus matrix (default: 0.75).
kmNStart	nstart parameter passed to kmeans. function. Can be set manually. By default it is 1000 for up to 2000 cells and 50 for more than 2000 cells.
kmMax	iter.max parameter passed to kmeans.
BPPARAM	(Optional) A BiocParallelParam object for parallel processing (default: bpparam()).

Value

A consensus matrix summarizing the clustering results across multiple sub-datasets.

Examples

library(scater)
library(BiocParallel)
library(splatter)

sce <- splatSimulate(group.prob = rep(1, 5)/5, sparsify = FALSE, 
        batchCells=100, nGenes=1000, method = "groups", verbose = FALSE, 
        dropout.type = "experiment")
sce <- logNormCounts(sce)
cores <- 2
logX <- as.matrix(logcounts(sce))
w <- rowVars_fast(logX, cores)
corMat <- getCorM("spearman", logcounts(sce), w, cores)
v <- doSVD(corMat, nCores=cores)
BPPARAM = MulticoreParam(cores)
consMtx <- runKM(logX, v, BPPARAM=bpparam())

khazum/ccImpute documentation built on July 26, 2024, 1:13 a.m.