top_by_intersect-ClusterSet-method: Select top_genes based on intersection with a list.

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Select top_genes based on intersection with a list.

Description

The clusterSet object contains a top_genes slot that can be used to display genes in heatmaps (see plot_heatmap function). Here the function select top_genes based on intersection with a list.

Usage

## S4 method for signature 'ClusterSet'
top_by_intersect(object, set = NULL, as_list = FALSE)

Arguments

object	A ClusterSet object.
set	A list to compare clusters to.
as_list	Return a list of clusters not a ClusterSet object.

Value

A ClusterSet object or a list (see as_list).

Examples

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

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

set <- c('MS4A1', 'ISG20', 'CD3D', 'SEC14L5', 'RPL11', 'RPL32')
pbmc3k_medium_clusters <- top_by_intersect(pbmc3k_medium_clusters, set=set)
pbmc3k_medium_clusters@top_genes

dputhier/scigenex documentation built on Feb. 18, 2025, 2:27 p.m.