cell_annotation_fn: Perform cell annotation via 'SingleR::SingleR()'.

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 cell annotation via SingleR::SingleR().

Description

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

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