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Perform cell annotation via SingleR::SingleR().

Source: R/cell_annotation.R
cell_annotation_fn.Rd

A new list column cell_annotation is added to cell_annotation_params, containing the returned DataFrames (one for each reference dataset) from SingleR::SingleR().

train_params and classify_params in cell_annotation_params are passed to SingleR::SingleR(), and internally to SingleR::trainSingleR() and SingleR::classifySingleR(), respectively.

Label pruning is performed via SingleR::pruneScores() after calling SingleR::SingleR(), with parameters defined in cell_annotation_params$prune_score_params.

Usage

cell_annotation_fn(
  cell_annotation_params,
  sce_test,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

cell_annotation_params

(input target) A tibble.

sce_test

(input target) A SingleCellExperiment object to predict cell labels in.

BPPARAM

A BiocParallel::BiocParallelParam object.

Value

A tibble. Output target: cell_annotation