Get pseudotime information

get_pseudotime(object, ...)

# Default S3 method
get_pseudotime(
  object,
  meta_data = NULL,
  embeddings = NULL,
  cluster_column = "cluster",
  cores = 1,
  seed = 1,
  start_cluster = NULL,
  end_cluster = NULL,
  verbose = TRUE,
  ...
)

# S3 method for class 'Seurat'
get_pseudotime(
  object,
  assay = "RNA",
  layer = "data",
  cluster_column = "cluster",
  reduction = "umap",
  start_cluster = NULL,
  end_cluster = NULL,
  ...
)

Arguments

object: The input data, a matrix with cells/samples by genes/features or a seurat object.
...: Arguments for other methods
meta_data: Input meta data.
embeddings: Embeddings information
cluster_column: The column used for slingshot.
cores: The number of cores to use for parallelization with foreach, default is 1.
seed: The random seed for cross-validation, default is 1.
start_cluster: The start cluster.
end_cluster: The end cluster.
verbose: Logical value, default is TRUE, whether to print progress messages.
assay: The assay used for slingshot.
layer: The layer used for slingshot.
reduction: The reduction used for slingshot.

Value

Pseudotime information corresponding to cells

Examples

if (FALSE) { # \dontrun{
data("example_matrix")
head(get_pseudotime(example_matrix))
} # }