Calculate and plot ROGUE index for a Seurat object, with inline filtering

Filters raw counts by minimum cells and genes, computes entropy and ROGUE metrics.

Usage

calcROGUE(
  obj,
  assay = "RNA",
  layer = "counts",
  downsample = 3000,
  min.cells = 10,
  min.genes = 10,
  anno_label = "celltype_broad",
  sample_label = "orig.ident",
  ...
)

Arguments

obj

A Seurat object with celltype_broad and orig.ident metadata.

assay

Assay name containing raw counts (default "RNA").

layer

Layer name for raw counts (default "counts").

downsample

Number of cells to downsample per group (default 3000).

min.cells

Minimum cells per gene for filtering (default 10).

min.genes

Minimum genes per cell for filtering (default 10).

anno_label

Cell type annotation label (default "celltype_broad").

sample_label

Sample label for grouping (default "orig.ident").

...

Additional arguments passed to rogue().or mc_rogue().

Value

An object returned by rogue(), invisibly.