Perform log normalization for counts — normalizeAssay • scider

Perform log normalization for counts

Usage

normalizeAssay(
  spe,
  transformation = c("log"),
  scale.factor = 1e+06,
  assay = "counts",
  name = "logcounts"
)

Arguments

spe: A SpatialExperiment object.
transformation: Choice of transformation. "Log" for log1p
scale.factor: Factor to multiply the count of each cell by. A single value or a numeric vector equal to number of cells
assay: Name of assay in spe to perform the transformation on
name: Name of the transformed assay

Value

A SpatialExperiment object

Examples

data("xenium_bc_spe")
spe <- normalizeAssay(spe)