clusterGenes {monocle}R Documentation

Clusters genes by pseudotime trend.

Description

This function takes a matrix of expression values and performs k-means clustering on the genes.

Usage

clusterGenes(
  expr_matrix,
  k,
  method = function(x) {     as.dist((1 - cor(Matrix::t(x)))/2) },
  ...
)

Arguments

expr_matrix

A matrix of expression values to cluster together. Rows are genes, columns are cells.

k

How many clusters to create

method

The distance function to use during clustering

...

Extra parameters to pass to pam() during clustering

Value

a pam cluster object

Examples

## Not run: 
full_model_fits <- fitModel(HSMM[sample(nrow(fData(HSMM_filtered)), 100),],  
   modelFormulaStr="~sm.ns(Pseudotime)")
expression_curve_matrix <- responseMatrix(full_model_fits)
clusters <- clusterGenes(expression_curve_matrix, k=4)
plot_clusters(HSMM_filtered[ordering_genes,], clusters)

## End(Not run)

[Package monocle version 2.21.1 Index]