top_genes-ClusterSet-method: Most co-expressed genes from each gene cluster
In dputhier/dbfmcl: The scigenex package (Single-Cell Informative GENe Explorer)

top_genes,ClusterSet-method

R Documentation

Most co-expressed genes from each gene cluster

Description

Extract the most highly co-expressed genes of each gene cluster.

Usage

## S4 method for signature 'ClusterSet'
top_genes(object, top = 20, fast = FALSE, distance_method = NULL)

Arguments

`object`	A `ClusterSet` object.
`top`	A value for the number of genes to select from each cluster.
`fast`	Use qlcMatrix::corSparse for pearson computation. Default to cor(). Default to FALSE for retro-compatibility.
`distance_method`	Overright the object distance_method (slot parameters$distance_method). Useful when object was created using cluster_set_from_matrix() for instance. One of c("kendall", "spearman", "cosine", "euclidean", "pearson") or NULL.

Value

A ClusterSet object.

Examples

# Set verbosity to 1 to display info messages only.
set_verbosity(1)

# Load a dataset
load_example_dataset('7871581/files/pbmc3k_medium_clusters')

# Store top genes in the object
pbmc3k_medium_clusters <- top_genes(pbmc3k_medium_clusters)

dputhier/dbfmcl documentation built on April 17, 2025, 4:41 a.m.