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Import sce_final_norm_clustering targets from drake caches.

Source: R/integration_integration.R
sce_int_import_fn.Rd

SingleCellExperiment objects are also checked for common HVG metric, and HVG combination method is validated.

Usage

sce_int_import_fn(
  integration_sources,
  hvg_combination = c("hvg_metric", "intersection", "union", "all")
)

Arguments

integration_sources

A list of sources to load sce_final_norm_clustering targets from. See 01_integration.yaml config for more details.

hvg_combination

A character scalar: method to use for combining HVGs:

  • "hvg_metric": combine gene variance or CV2, e.g. all samples had HVG_METRIC set to "gene_var"(scran::combineVar()) or "gene_cv2" (scran::combineCV2()).

  • "intersection": make intersection of HVGs.

  • "union": make union of HVGs.

  • "all": take all HVGs from all samples (without duplicates).

Value

A list of SingleCellExperiment objects. Output target: sce_int_import

The following items of metadata() of each imported SingleCellExperiment object are added or modified:

  • single_sample_path, single_sample_path_type, single_sample_name, single_sample_description, hvg_rm_cc_genes, hvg_cc_genes_var_expl_threshold: taken from INTEGRATION_SOURCES config parameter.

  • hvg_combination: the value of the hvg_combination function argument.