Main mapping function — .map_celltypes • scFlow

Main mapping function

.map_celltypes(
  ctdToMap,
  ctdToMapAgainst = MAGMA.Celltyping::ctd_Tasic,
  inputSpecies = "human",
  mapAgainstSpecies = "mouse",
  annotLevel = 1,
  numTopMarkers = 50,
  mappingLevel = 2,
  reps = 1000
)

Arguments

ctdToMap: ctd for current expt
ctdToMapAgainst: the ctd to map against
inputSpecies: "human" or "mouse"
mapAgainstSpecies: "human" or "mouse"
annotLevel: level of annotation
numTopMarkers: number of top markers to consider
mappingLevel: level of mapping

Value

sce a SingleCellExperiment object annotated with sample metadata

See also

Other clustering and dimensionality reduction: .get_x_most_specific_genes(), .map_celltypes_with_ewce(), cluster_sce(), map_custom_celltypes(), reduce_dims_sce()

Author

Nathan Skene / Combiz Khozoie