Integration Workflow

Integrate multiple seurat objects and save to file

integration_workflow(
  batches,
  excluded_cells = NULL,
  resolution = seq(0.2, 2, by = 0.2),
  experiment_name = "default_experiment",
  organism = "human",
  ...
)

Arguments

batches

seurat objects for all batches provided as a list. If named, the resulting integrated object will be identified with corresponding values in 'batch' metadata

excluded_cells

named list of cells to exclude

resolution

value(s) to control the clustering resolution via Seurat::FindMarkers

experiment_name

arbitrary name to identify experiment

organism

either "human" or "mouse"

...

Examples

batches <- panc8 %>%
    Seurat::SplitObject(split.by = "tech")

integrated_seu <- integration_workflow(batches)
#> [13:34:50] Logging Technical Details...
#> [13:34:50] Logging Technical Details...
#> Error in map_chr(batches, list("misc", "experiment", "organism")): could not find function "map_chr"