normalize: Normalize expression using pre-computed size factors

In acidgenomics/r-acidsinglecell: Acid Genomics Single Cell Experiment

Normalize expression using pre-computed size factors

Description

This function calculates log-normalized size-factor-adjusted counts that are defined in logcounts() from the raw, non-normalized count matrix defined in counts().

Usage

normalize(object, ...)

## S4 method for signature 'SingleCellExperiment'
normalize(object)

Arguments

object	Object.
...	Additional arguments.

Details

If no library size factors are defined in sizeFactors(), these values will be computed internally automatically using scuttle::computeLibraryFactors().

Value

Modified object.

Note

Updated 2022-03-02.

See Also

• AcidExperiment::estimateSizeFactors().

• scuttle::computeLibraryFactors().

• scuttle::logNormCounts().

• scuttle::librarySizeFactors().

• scuttle::geometricSizeFactors().

• scuttle::medianSizeFactors().

• Seurat::NormalizeData().

• monocle3::preprocess_cds().

• monocle3::normalized_counts().

• SingleCellExperiment::normcounts().

• SingleCellExperiment::logcounts().

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
object <- normalize(object)
head(BiocGenerics::sizeFactors(object))
SingleCellExperiment::logcounts(object)[seq_len(2L), seq_len(2L)]

acidgenomics/r-acidsinglecell documentation built on March 30, 2024, 5:39 a.m.