cKmeansWrapperSubsample: Wrapper for constrained K-means on subsampled data

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

Wrapper for constrained K-means on subsampled data

Description

This fuction is a wrapper for the constrained Kmeans algorithm using 'lcvqe' from the 'conclust' package. This function will subset each cohort down to that with the smallest number of observations.This function is not meant to be run individually, but as a 'clustFunc' argument for running 'K2preproc()', 'runK2Taxonomer()', and 'K2tax()'.

Usage

cKmeansWrapperSubsample(dataMatrix, clustList)

Arguments

dataMatrix	An P x C numeric matrix of data. Where C is the number of cohort labels.
clustList	List of objects to use for clustering procedure. 'eMat'P x N Expression matrix of data set. See '?Biobase::exprs()'. 'labs'Vector of cohort labels of observations in data set, corresponding to columns of 'clustList$eMat'.

Value

A character string of concatenated 1's and 2's pertaining to the cluster assignment of each column in dataMatrix.

References

\insertRef

reed_2020K2Taxonomer \insertRefcKmK2Taxonomer

Examples

dat <- scRNAseq::ReprocessedAllenData(assays='rsem_tpm')[seq_len(50),]

eSet <- ExpressionSet(assayData=assay(dat))
pData(eSet) <- as.data.frame(colData(dat))
exprs(eSet) <- log2(exprs(eSet) + 1)

## Subset for fewer cluster labels for this example
eSet <- eSet[, !is.na(eSet$Primary.Type) &
            eSet$Primary.Type %in% c('L4 Arf5',
                'L4 Ctxn3', 'L4 Scnn1a', 'L5 Ucma', 'L5a Batf3')]

## Create cell type variable with spaces
eSet$celltype <- gsub(' ', '_', eSet$Primary.Type)

## Create clustList
cL <- list(
    eMat=exprs(eSet),
    labs=eSet$celltype,
    maxIter=10)

## Run K2preproc to generate generate data matrix
## with a column for each celltype.
K2res <- K2preproc(eSet,
                cohorts='celltype',
                featMetric='F',
                logCounts=TRUE)
dm <- K2data(K2res)

## Generate K=2 split with constrained K-means
cKmeansWrapperSubsample(dm, cL)

montilab/K2Taxonomer documentation built on Jan. 25, 2024, 4:29 p.m.