Normalizes m/z intensity data stored in a SpaMTP Seurat Object

This function can be used for normalising data already stored in a SpaMTP Seurat Object. Normalisation methods include total ion count (TIC), log normalisation and counts per million (RC).

Usage

NormalizeSMData(
  data,
  normalisation.type = "TIC",
  scale.factor = NULL,
  assay = "Spatial",
  slot = "counts",
  verbose = TRUE
)

Arguments

data

Seurat Object to be normalized.

normalisation.type

Character string defining the normalization method to run. Options are either c("TIC", "LogNormalize", "RC") which represent Total Ion Current (TIC) normalization, Log Normalization or counts per million (RC), respectively (default = "TIC").

scale.factor

Numeric value that sets the scale factor for pixel/spot level normalization. Following normalization the total intensity value across each pixel will equal this value. If scale.factor = NULL, TIC normalization will use a scale factor = number of m/z and Log Normalisation will use a scale factor = 10000 (default = NULL).

assay

Character string defining the name of the Seurat Object assay to pull the corresponding intensity data from (default = "Spatial").

slot

Character string defining the name of the slot within the Seurat Object assay to pull the corresponding intensity data from (default = "counts").

verbose

Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Value

A Seurat Object with intensity values normalized. Normalized data is stored in the $data slot of the specified assay

Examples

# normalised_data <- NormalizeSMData(SeuratObject)