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Performs pathway activity analysis of Spatial transcriptomics data and subsequent clustering with Seurat clustering. Input data is a Seurat object.

Source: R/fast_psf_functions.R
spatial_psf_analysis.Rd

Performs pathway activity analysis of Spatial transcriptomics data and subsequent clustering with Seurat clustering. Input data is a Seurat object.

Usage

spatial_psf_analysis(
  spatial_obj,
  pathway_collection,
  gene_symbol_to_entrez,
  nthreads = 1,
  return_only_shiny_vars = TRUE
)

Arguments

spatial_obj

Seurat object of spatial transcriptomic dataset.

pathway_collection

pathway collection list which will be used of PSF analysis

gene_symbol_to_entrez

gene id conversion vector where names are the gene identifiers corresponding to count matrix row names and objects are entrez gene ids.

nthreads

integer, the number of CPUs to use for calculation. Default value is 1.

return_only_shiny_vars

when set tot TRUE list of variables will be return which can be used to lunch PSF spatial browser shiny app. Default value is TRUE.