Normalize expression using pre-computed size factors

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 SingleCellExperiment
normalize(object)

Arguments

object

Object.

...

Additional arguments.

Value

Modified object.

Details

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

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)
#> → Generating "sizeFactors" using scuttle::`computeLibraryFactors()`.
#> → Generating "logcounts" assay using scuttle::`logNormCounts()`.
head(BiocGenerics::sizeFactors(object))
#>   cell001   cell002   cell003   cell004   cell005   cell006 
#> 1.1197719 1.3368575 1.3180723 0.9077306 0.6311123 1.5813429 
SingleCellExperiment::logcounts(object)[seq_len(2L), seq_len(2L)]
#> 2 x 2 sparse Matrix of class "dgCMatrix"
#>           cell001   cell002
#> gene001  7.272422  7.168646
#> gene002 10.265281 10.230713