createGiottoXeniumObject_subcellular: Create a Xenium Giotto object from subcellular info
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

createGiottoXeniumObject_subcellular

R Documentation

Create a Xenium Giotto object from subcellular info

Subcellular workflow for createGiottoXeniumObject

createGiottoXeniumObject_subcellular(
  data_list,
  key_list = NULL,
  qv_threshold = 20,
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

`data_list`	list of data loaded by `load_xenium_folder`
`key_list`	regex-based search keys for feature IDs to allow separation into separate giottoPoints objects by feat_type
`qv_threshold`	Minimum Phred-scaled quality score cutoff to be included as a subcellular transcript detection (default = 20)
`instructions`	list of instructions or output result from `createGiottoInstructions`
`cores`	how many cores or threads to use to read data if paths are provided
`verbose`	be verbose when building Giotto object