Normalise Marker Intensities (SpatialCellData) — NormaliseData • phenoscapR

Normalises marker intensities and stores the result in the data slot. Raw counts remain unchanged.

Usage

NormaliseData(
  object,
  method = c("zscore", "minmax", "quantile"),
  markers = NULL
)

Arguments

object: An SpatialCellData-class object.
method: Character. "zscore" (default), "minmax", or "quantile".
markers: Character vector or NULL. Markers to normalise. If NULL, all markers are normalised.

Value

An SpatialCellData-class with updated data slot.

Examples

counts <- matrix(rnorm(40, 500, 100), nrow = 20,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(20), y = runif(20))
obj <- CreateSpatialObject(counts, coords)
obj <- NormaliseData(obj, method = "zscore")