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Write metabolomics data release

Source: R/metabolomics_qc.R
write_metabolomics_releases.Rd

Write out metabolomics data releases. Doesn't check whether data has been submited according to guidelines

Usage

write_metabolomics_releases(
  input_results_folder,
  cas,
  folder_name = "motrpac_release",
  folder_root = NULL,
  version_file = "v1.0",
  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")

folder_name

(char) output files name. Must have a .yaml extension.

folder_root

(char) absolute path to write the output files. Default: current directory

version_file

(char) file version number (v#.#)

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. Releases should be written from batches already validated with validate_metabolomics(), which runs the full refmet_name validation by default.

verbose

(logical) TRUE (default) shows messages

Value

bic release folder/file structure PHASE/OMICS/TCODE_NAME/ASSAY/ and file names, including:

  • motrpac_YYYYMMDD_phasecode_tissuecode_omics_assay_file-details.txt where files-details can be:

  • named-experimentalDetails.txt

  • named-metadata-metabolites.txt

  • metadata-samples.txt

  • named-results.txt

Examples

if (FALSE) { # \dontrun{
write_metabolomics_releases(input_results_folder = "/path/to/PROCESSED_YYYYMMDD/", 
cas = "umichigan")
} # }