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Normalise counts via pooling-based size factors

Source: R/method-L1_analysis_tracks.R
normalize_counts.Rd

Computes size factors using computePooledFactors and applies log-normalisation via logNormCounts. If a logcounts assay already exists it is overwritten with a warning.

Usage

normalize_counts(
  sce,
  min_cluster_size = 100L,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

sce

A SingleCellExperiment with a counts assay.

min_cluster_size

Integer scalar. Minimum cluster size for quickCluster used to seed the pooling. Defaults to 100.

BPPARAM

A BiocParallelParam for parallelisation.

Value

The input SCE with sizeFactors() set and a logcounts assay added.