sce_int_df_fn: Perform integration of single-samples.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Perform integration of single-samples.

Description

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.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.