Perform integration of single-samples.

Usage

sce_int_df_fn(
  sce_int_multibatchnorm,
  integration_methods_df,
  BPPARAM = BiocParallel::SerialParam()
)

sce_int_multibatchnorm: (input target) A SingleCellExperiment object processed by batchelor::multiBatchNorm().
integration_methods_df: (input target) A tibble: transformed from INTEGRATION_METHODS parameter in 01_integration.yaml config.
BPPARAM: A BiocParallel::BiocParallelParam object.

A modified integration_methods_df tibble with appended integrated SingleCellExperiment object. Output target: sce_int_df

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

single_samples_metadata_df: a tibble with information about individual samples:
- sample_name, description, cache_path, n_features, hvg_rm_cc_genes, hvg_cc_genes_var_expl_threshold, has_filtered_doublets, max_doublet_score, Samples: vectors merged from metadata() of individual samples.
- n_cells: number of cells.
- hvg_ids, hvg_rm_cc_genes_ids: lists of character vectors of HVG / removed HVG IDs.
- cell_groupings: list of cell grouping definitions.
- hvg_metric: list of HVG metrics.
hvg_rm_cc_genes, int_method_name, int_param: taken from integration method parameters.
hvg_rm_cc_genes_ids: a character scalar of removed CC-related genes' IDs.