Load metabolomics batch — load_metabolomics

Open, check, and return all metabolomics files

Usage

load_metabolomics_batch(
  input_results_folder,
  cas,
  refmet_validation = FALSE,
  verbose = TRUE
)

Arguments

input_results_folder: (char) Path to the PROCESSED_YYYYMMDD folder
cas: (char) Chemical Analytical Site code (e.g "umichigan")
refmet_validation: (logical) FALSE (default) skips the refmet_name validation against the Metabolomics Workbench API (one request per metabolite, slow) while running every other check. Set to TRUE to also validate the refmet_name ids. Full refmet_name validation belongs to validate_metabolomics(), which should be run before loading a batch.
verbose: (logical) TRUE (default) shows messages

Value

(list of data.frames) List of all the data frames

Examples

if (FALSE) { # \dontrun{
here <- load_metabolomics_batch(input_results_folder = "/path/to/PROCESSED_YYYYMMDD/",
                                cas = "cassite")
} # }