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Perform integration of single-samples.

Usage

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

Arguments

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.

Value

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.