clusterGenes {monocle} | R Documentation |
This function takes a matrix of expression values and performs k-means clustering on the genes.
clusterGenes(expr_matrix, k, method = function(x) { as.dist((1 - cor(Matrix::t(x)))/2) }, ...)
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 |
a pam cluster object
## 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)