Performs TMM normalization between categories based on a specified ident
Source:R/SMPreprocessing.R
TMMNormalize.RdThis function is mainly used for normalising a merged SpaMTP Seurat Object containing multiple samples.
Usage
TMMNormalize(
combined.obj,
ident,
refIdent,
normalisation.type = "CPM",
CPM.scale.factor = 1e+06,
assay = "Spatial",
slot = "counts",
verbose = FALSE
)Arguments
- combined.obj
Seurat object that contains groups being normalized.
- ident
Character string defining the column name or ident group to normalize between.
- refIdent
Character string specifying one class/group type to use as a reference for TMM normalisation.
- normalisation.type
Character string defining the normalization method to run. Options are either c("CPM", "TIC", "LogNormalize") which represent counts per million (CPM), Total Ion Current (TIC) normalization or Log Normalization, respectively (default = "CPM").
- CPM.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 (default = 1e6).
- 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 = FALSE).