markers_cluster_seurat: markers_cluster_seurat

In CIARA: Cluster Independent Algorithm for Rare Cell Types Identification

markers_cluster_seurat

Description

The Seurat function FindMarkers is used to identify general marker for each cluster (specific cluster vs all other cluster). This list of markers is then filtered keeping only the genes that appear as markers in a unique cluster.

Usage

markers_cluster_seurat(seurat_object, cluster, cell_names, number_top)

Arguments

seurat_object	Seurat object as returned by cluster_analysis_sub or by cluster_analysis_integrate_rare.
cluster	Vector of length equal to the number of cells, with cluster assignment.
cell_names	Vector of length equal to the number of cells, with cell names.
number_top	Integer. Number of top marker genes to keep for each cluster.

Value

List of three elements. The first is a vector with number_top marker genes for each cluster. The second is a vector with number_top marker genes and corresponding cluster. The third element is a vector with all marker genes for each cluster.

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://www.rdocumentation.org/packages/Seurat/versions/4.0.1/topics/FindMarkers

CIARA documentation built on March 18, 2022, 6:48 p.m.