Create 10x VisiumHD Giotto Object — createGiottoVisiumHDObject • Giotto

Given the path to a VisiumHD output folder, creates a Giotto object

createGiottoVisiumHDObject(
  visiumHD_dir = NULL,
  expr_data = c("raw", "filter"),
  gene_column_index = 1,
  instructions = NULL,
  expression_matrix_class = c("dgCMatrix", "DelayedArray"),
  cores = NA,
  verbose = FALSE
)

Arguments

expr_data: raw or filtered data (see details)
gene_column_index: which column index to select (see details)
expression_matrix_class: class of expression matrix to use (e.g. "dgCMatrix", "DelayedArray")
cores: how many cores or threads to use to read data if paths are provided
verbose: be verbose
VisiumHD_dir: full path to the exported visiumHD directory

Value

giotto object

Details

expr_data: raw will take expression data from raw_feature_bc_matrix and filter from filtered_feature_bc_matrix
gene_column_index: which gene identifiers (names) to use if there are multiple columns (e.g. ensemble and gene symbol)