as.Seurat.extras: Convert single cell experiment to Seurat

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

Convert single cell experiment to Seurat

Description

Convert single cell experiment to Seurat

Usage

## S3 method for class 'cell_data_set'
as.Seurat(
  x,
  counts = "counts",
  data = NULL,
  assay = "RNA",
  project = "cell_data_set",
  loadings = NULL,
  clusters = NULL,
  ...
)

Arguments

loadings	Name of dimensional reduction to save loadings to, if present; defaults to first dimensional reduction present (eg. SingleCellExperiment::reducedDimNames(x)[1]); pass NA to suppress transfer of loadings
clusters	Name of clustering method to use for setting identity classes

Details

The cell_data_set method for as.Seurat utilizes the SingleCellExperiment method of as.Seurat to handle moving over expression data, cell embeddings, and cell-level metadata. The following additional information will also be transfered over:

• Feature loadings from cds@reduce_dim_aux$gene_loadings will be added to the dimensional reduction specified by loadings or the name of the first dimensional reduction that contains "pca" (case-insensitive) if loadings is not set

• Monocle 3 clustering will be set as the default identity class. In addition, the Monocle 3 clustering will be added to cell-level metadata as “monocle3_clusters”, if present

• Monocle 3 partitions will be added to cell-level metadata as “monocle3_partitions”, if present

• Monocle 3 pseudotime calculations will be added to “monocle3_pseudotime”, if present

• The nearest-neighbor graph, if present, will be converted to a Graph object, and stored as “assay_monocle3_graph”

See Also

as.Seurat.SingleCellExperiment

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.