read_data_folder: Read a structured folder of exported data

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Read a structured folder of exported data

Description

Read the exported folder of a spatial method and detect the presence of needed files. NULL values denote missing items.

Usage

read_data_folder(
  spat_method = NULL,
  data_dir = NULL,
  dir_items,
  data_to_use,
  load_format = NULL,
  require_data_DT,
  cores = NA,
  verbose = TRUE
)

read_merscope_folder(merscope_dir, data_to_use, cores = NA, verbose = TRUE)

Arguments

spat_method	spatial method for which the data is being read
data_dir	exported data directory to read from
dir_items	named list of directory items to expect and keywords to match
data_to_use	which type(s) of expression data to build the gobject with
require_data_DT	data.table detailing if expected data items are required or optional for each data_to_use workflow
cores	cores to use
verbose	be verbose

Details

Steps performed:

• 1. detection of items within data_dir by looking for keywords assigned through dir_items

• 2. check of detected items to see if everything needed has been found. Dictionary of necessary vs optional items for each data_to_use workflow is provided through require_data_DT

• 3. if multiple filepaths are found to be matching then select the first one. This function is only intended to find the first level subdirectories and files.

Functions

• read_merscope_folder(): Read a structured MERSCOPE folder

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.