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Create a scdown object

Source: R/object.R
scdown.Rd

scdown() standardizes annotation-after single-cell inputs into a compact object for cluster interpretation within one dataset. Supported inputs are:

Usage

scdown(
  x,
  annotation_col = "annotation",
  sample_col = "sample",
  reduced_dim = "UMAP",
  embedding = NULL,
  assay_name = NULL,
  expression_layer = NULL,
  signatures = NULL,
  marker_panels = NULL,
  lr_pairs = NULL
)

Arguments

x

Input data.

annotation_col

Column containing cluster or annotation labels.

sample_col

Optional column containing sample identifiers.

reduced_dim

Reduced-dimension name used when extracting embeddings from Bioconductor or Seurat objects.

embedding

Optional data frame with cell, UMAP1, and UMAP2.

assay_name

Optional assay name for SingleCellExperiment or Seurat.

expression_layer

Optional Seurat layer or slot name.

signatures

Optional named list of custom signatures.

marker_panels

Optional named list of custom marker panels.

lr_pairs

Optional data frame with ligand, receptor, and pathway.

Value

An object of class scdown_obj.

Details

  • a long table with cell, gene, and value

  • a list with expr, cells, and optional embedding

  • a SingleCellExperiment

  • a Seurat object