map_celltypes_sce: Map cluster celltypes with EWCE

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Map cluster celltypes with EWCE

Description

Map cluster celltypes with EWCE

Usage

map_celltypes_sce(
  sce,
  ctd_folder,
  cells_to_sample = 10000,
  clusters_colname = "clusters",
  species = getOption("scflow_species", default = "human"),
  save_path = tempdir(),
  annotation_level = 1,
  reps = 1000,
  ctd_species = NULL,
  num_markers = 50,
  label_index = 1
)

Arguments

sce	a SingleCellExperiment
ctd_folder	path to a folder with ctd RDS file
cells_to_sample	total cells to consider for gene enrichment
clusters_colname	the name of the colData column with cluster number
species	specify species of analysis dataset
save_path	The directory where the generated ctd file produced by EWCE is saved. Default is a temp directory
annotation_level	The level(s) of annotation required. Integer for single CTD/level. For multi-CTD/level a named list, names are the CTD file names (without file extension) and elements are vectors of levels. Levels must present in the provided CTD(s). The first name and level will also be used as the primary annotation for automated reporting and will be returned in 'cluster_celltype' column data.
reps	Number of bootstrap repetitions for EWCE. For publishable results set >=10000.
ctd_species	Specify species used to build CTD if different from species. If multiple CTDs are used with differing species specify as a named list where names are the CTD file names (without file extension) and elements are the species. Must be 'human', 'mouse' or listed in EWCE::list_species()$id.
num_markers	Number of cluster markers used to identify cell type
label_index	The annotation_level index to use to name the cluster_celltype. Default is 1

Value

sce a SingleCellExperiment object annotated with celltypes/metadata

Author(s)

Nathan Skene / Combiz Khozoie / Michael Thomas

See Also

Other Celltype annotation: find_marker_genes(), model_celltype_freqs()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.