filter_nb_supporting_cells: Filter out cluster supported by few cells.

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

Filter out cluster supported by few cells.

Description

This function filters out the gene clusters based on the number of cells expressing a certain percentage of genes present in this gene cluster.

Usage

filter_nb_supporting_cells(
  object = NULL,
  min_nb_supporting_cell = 3,
  min_pct_gene_expressed = 50
)

Arguments

object	A ClusterSet object.
min_nb_supporting_cell	An integer indicating the minimum number of cell supporting a cluster. A cell supports a cluster if it expresses at least min_pct_gene_expressed % of the genes from the cluster.
min_pct_gene_expressed	See min_nb_supporting_cell argument.

Value

A ClusterSet object where clusters that did not pass the filter have been removed.

Examples

load_example_dataset("7871581/files/pbmc3k_medium_clusters")
new_cs <- filter_nb_supporting_cells(pbmc3k_medium_clusters, 3, 50)

dputhier/scigenex documentation built on Jan. 29, 2024, 3:40 p.m.