ClusterClassification: ClusterClassification

In alexthiery/scHelper: R package containing helper functions for single cell analysis

ClusterClassification

Description

This function retrieves cluster classifications using cell module score columns in seurat object. Clusters are classiffied as a given cell type if the median for a given cell type falls outside the provided quantile.

Usage

ClusterClassification(
  seurat_obj = seurat_data,
  group_by = "seurat_clusters",
  cell_type_markers = cell_type_markers,
  quantile = 0.8,
  assay = "RNA",
  annotation_name = "scHelper_cell_type",
  force_assign = FALSE,
  plot_path = "scHelper_log/",
  ...
)

Arguments

seurat_obj	Seurat object
group_by	column to group cells by
quantile	Percent quantile to plot on bar plots. Must be a single value representing the upper percent quantile
annotation_name	Name of column to be annotated with corresponding cell types
force_assign	Boolean for whether to force assign cell identity to clusters which do not pass the filtering threshold
plot_path	Directory to plot log files
...	Additional options to be passed to grid.arrange
cell_types	column names for cell type module scores found in [e-mail]

Value

array of clusters which are outliers

alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.