Create a singular multiomics assay by merging data from multiple assays.

Combines the scale.data slots from multiple assays in a SpaMTP Seurat object into a single new assay. Useful for integrating multiple modalities (e.g. transcriptomics, proteomics, metabolomics) that have already been scaled.

Usage

CreateMergedModalityAssay(
  SpaMTP,
  assays.to.merge,
  new.assay = "merged",
  return.original = TRUE,
  verbose = FALSE
)

Arguments

SpaMTP: A SpaMTP Seurat object that contains atleast two assays to be merged.
assays.to.merge: A character vector specifying the names of assays whose scale.data slots should be merged. At least two assay names must be provided and both must contain the scale.data slot, for example: assays.to.merge = c("SPM", "SPT").
new.assay: A character string specifying the name of the new assay to be created (default = "merged").
return.original: Boolean value defining if the returned SpaMTP Seurat object will contain the original individual assays. If the data size is large it is recommended to set to False (default = TRUE).
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 SpaMTP Seurat object containing a new assay with the merged scaled data values.

Details

This function assumes that each specified assay has been processed with Seurat::ScaleData() (or an alternative scaling method), and that their scale.data slots contain numeric matrices. The merged assay will use the row-bound scale.data matrices as the counts, data, and scale.data slots.

Examples

# merged_obj <- CreateMergedModalityAssay(SpaMTP = spamtp_obj, assays.to.merge = c("SPM", "SPT"),new.assay = "merged")