Relative counts normalisation.

Source: R/logTransf.R

Do log1p normalisation by default.

logTransf(
  sce,
  scalFactor = 10000,
  assayName = "counts",
  targetAssay = "log1p",
  use_log1p = TRUE,
  sparse = TRUE
)

Arguments

sce

SingleCellExperiment object.

scalFactor

Scale factor to inflate relative counts.

assayName

Character.

targetAssay

Character.

use_log1p

Logical. Use shifted log (log1p) transform, using raw counts instead of relative counts.

sparse

Store the transformed assay as sparse matrix or not.

Value

A SingleCellExperiment object containing a new assay after relative counts normalisation.

Examples

sce <- scuttle::mockSCE(ncells = 20, ngenes = 10)
sce <- logTransf(sce, targetAssay = "log1p")
assay(sce, "log1p")[1:3, 1:3]