Prepare proseg Seurat data

Initial formatting of proseg re-segmented data to work with Seurat and Kandinsky

prepare_proseg_seurat(
  path = NULL,
  dataset.id = NULL,
  pattern = NULL,
  fovs = NULL,
  tech = c("cosmx", "merscope", "xenium")
)

Arguments

path

character string specifying the path to the proseg input files directory

dataset.id

character string that will be used to name the output Seurat object identity

pattern

character string that will be used as a key to identify proseg input file names in case when input files from multiple proseg samples/slides are stored in the same directory

fovs

vector of FOV identifiers to subset for downstream analysis.

tech

character string specifying the technology used to generate the data processed with proseg. Must be one of the following: "cosmx", "merscope", "xenium"

Value

a Seurat object containing proseg expected count matrix, metadata, and additional files/file paths to be used for downstream analysis with Kandinsky functions

Details

This function will use proseg raw input data (generated from either CosMx, Xenium, or Merscope datasets) to build a new Seurat object. All proseg input files must be stored in the same folder that will be specified to call the function

See also

Other prepare_data: prepare_cosmx_seurat(), prepare_g4x_seurat(), prepare_merscope_seurat(), prepare_slideseq_seurat(), prepare_visiumHD_seurat(), prepare_visium_seurat(), prepare_xenium_seurat()