Map cluster celltypes with EWCE

Map cluster celltypes with EWCE

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

See also

Other Celltype annotation: find_marker_genes(), model_celltype_freqs()

Author

Nathan Skene / Combiz Khozoie / Michael Thomas