SpaCET deconvolution using an `screference`

Usage

spacet_deconvolute(
  spatial_obj,
  scref,
  cancerType,
  sc_lineage_tree = NULL,
  sc_nCellEachLineage = 100,
  ncores = parallel::detectCores() - 1
)

Arguments

spatial_obj: an `Seurat` object with a Spatial assay
scref: an `screference` object containing single-cell reference data
cancerType: A character string specifying the type of cancer.
sc_lineage_tree: An optional data frame representing the single-cell lineage tree. Default is NULL.
sc_nCellEachLineage: An integer specifying the number of cells for each lineage. Default is 100.
ncores: An integer specifying the number of cores to use for parallel processing. Default is parallel::detectCores() - 1.

Details

This function utilizes the SpaCET package to perform deconvolution. It first creates a SpaCET object with spatial transcriptomics data, and then performs deconvolution using matched single-cell RNA-seq data.

For detailed documentation on the underlying SpaCET functions, refer to the original SpaCET package documentation: - create.SpaCET.object - SpaCET.deconvolution.matched.scRNAseq