Selects the clusters that belong to a given percentile of the clusters with the largest physically interacting cells proportion based on FSC ratio thresholding.
By default, the top 20 percent of clusters are chosen. Consider using ratio_cluster_plot to evaluate the choice of percentile cutoff.
Usage
select_dbt(
obj,
clusters = "seurat_clusters",
ratio = "ratio_anno",
ratio_high = "Ratio_high",
assay = "FACS",
quantile = 0.8,
selected_clusters = "doublet_clusters"
)Arguments
- obj
The Seurat object.
- clusters
The meta.data column containing the cluster labels (Default: seurat_clusters).
- ratio
The meta.data column with the classification of cells into ratio_high and ratio_low using the FSC ratio (FSC.A/FSC.H) and a thresholding method.
- ratio_high
The character string that indicates cells with a FSC ratio (FSC.A/FSC.H) above the threshold determined with
calculateThresholdwithin the meta.data column.- assay
The Seurat assay containing FACS data.
- quantile
The desired percentile cutoff above which clusters are classified as physically interacting cell clusters (Default 0.8, meaning top 20 percent of clusters are chosen).
- selected_clusters
Character vector for the misc slot in the Seurat object that will contain the cluster numbers of the selected physically interacting cell clusters (Default: "doublet_clusters").