Load MERSCOPE data from folder

Source: R/convenience_general.R

Load MERSCOPE data from folder

.load_merscope_folder(
  dir_items,
  data_to_use,
  polygon_format,
  fovs = NULL,
  poly_z_indices = 0:6,
  version = 1,
  cores = NA,
  verbose = TRUE
)

.load_merscope_folder_subcellular(
  dir_items,
  data_to_use,
  polygon_format,
  cores = NA,
  poly_z_indices = 0L:6L,
  version = 1,
  verbose = TRUE,
  fovs = NULL
)

.load_merscope_folder_aggregate(
  dir_items,
  data_to_use,
  cores = NA,
  verbose = TRUE
)

Arguments

dir_items

list of full filepaths from .read_merscope_folder

data_to_use

which of either the 'subcellular' or 'aggregate' information to use for object creation

polygon_format

format of the boundary files, either 'parquet' or 'hdf5' (v2 only)

poly_z_indices

which z-indices to use for the polygons (Default 0:6 for v2, 1:7 for v1)

version

integer. Version of logic to use (1 = Legacy/Original, 2 = New/Optimized)

cores

how many cores or threads to use to read data if paths are provided

verbose

be verbose when building Giotto object

Value

list of loaded-in MERSCOPE data

Functions

  • .load_merscope_folder_subcellular(): Load items for 'subcellular' workflow

  • .load_merscope_folder_aggregate(): Load items for 'aggregate' workflow