Filter out gene clusters containing few genes

Source: R/filter_gene_clusters.R

This function filters out gene clusters from a ClusterSet object based on their size.

filter_cluster_size(object = NULL, min_cluster_size = 5, rename = FALSE)

Arguments

object

A ClusterSet object.

min_cluster_size

An integer indicating the minimum size for a clusters to be kept.

rename

Should cluster be renamed.

Value

A ClusterSet object where clusters not passing the filter have been removed.

Examples

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

# Load a dataset
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
#> |-- INFO :  Dataset 7871581/files/pbmc3k_medium_clusters was already loaded. 
clust_size(pbmc3k_medium_clusters)
#>  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 
#> 51 49 45 24 20 18 14 14 14 12  7  7  6  5  5 
# Remove the cluster with less than 20 genes
clust_set <- filter_cluster_size(pbmc3k_medium_clusters,
                                 min_cluster_size = 20)
#> |-- INFO :  10  clusters with less than 20 were filtered out. 
#> |-- INFO :  Number of clusters left 5 
clust_size(clust_set)
#>  1  2  3  4  5 
#> 51 49 45 24 20