Wrapper for hierarchical clustering

This fuction is a wrapper for the hclust, dist, and cutree functions. It outputs a string of a concatenated vector of 1's and 2's indexed by column. This function is not meant to be run individually, but as a 'clustFunc' argument for running `K2preproc()`, `runK2Taxonomer()`, and `K2tax()`.

hclustWrapper(dataMatrix, clustList)

Arguments

dataMatrix	An P x N numeric matrix of data.
clustList	Named list of objects to use for clustering procedure. Or `NULL` to use Euclidean distance with Ward's method. 'distMetric'Distance method to use. See ?dist. 'aggMethod'Agglomerative method to use. See ?hclust.

Value

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

References

Reed ER, Monti S (2020). “Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.” Bioinformatics. doi: 10.1101/2020.11.05.370197 , http://biorxiv.org/lookup/doi/10.1101/2020.11.05.370197.

Examples

## Read in sample ExpressionSet
require(Biobase)
data('sample.ExpressionSet')

## Extrat subset of data matrix
dm <- exprs(sample.ExpressionSet)[seq_len(50),]

## Create list of objects for clustering procedure.
cL <- list(distMetric='euclidean', aggMethod='ward.D2')

## Generate K=2 split with hierarchical clustering
hclustWrapper(dm, cL)
#> [1] "12111212212212121111112122"