QA functions for the MoTrPAC community

validate_metabolomics

R Documentation

Validate a Metabolomics submission

Description

Validate a Metabolomics submission

Usage

validate_metabolomics(
  input_results_folder,
  cas,
  return_n_issues = FALSE,
  full_report = FALSE,
  f_proof = FALSE,
  printPDF = TRUE,
  out_qc_folder = NULL,
  dmaqc_shipping_info = NULL,
  dmaqc_phase2validate = FALSE,
  verbose = TRUE
)

Arguments

`input_results_folder`	(char) path to the PROCESSED folder to check
`cas`	(char) CAS code
`return_n_issues`	(logical) if `TRUE` returns the number of issues
`full_report`	(logical) if `FALSE` (default) it returns only the total number of issues. If `TRUE` returns the details of the number of issues (by group of files, e.g., results, metadata_metabolites, etc)
`f_proof`	(logical) generate charts including: Sample intensity distribution Unique ID counts NA values
`printPDF`	(logical) if `f_proof = TRUE`, then `printPDF = TRUE` (default) prints plots to pdf file and argument `out_qc_folder` should be provided.
`out_qc_folder`	(char) Folder to save the pdfs (if `printPDF = TRUE`). It will create the folder if it doesn't exist. If this argument is not provided, the files will be written to the working directory
`dmaqc_shipping_info`	(char) File path to the DMAQC file. Only the BIC can use this argument
`dmaqc_phase2validate`	(char) Provide phase to validate. This argument is not required since it should be extracted from the input folder or from the new required file `metadata_phase.txt`. Please, ignore. However, if this argument is provided, it will take priority and this will be the phase. `metadata_phase.txt` will be ignored). Examples Folder with `PASS1A-06`: type either `PASS1A-06` or leave it `NULL` Both `PASS1A-06` and `PASS1C-06`: type `PASS1A-06\|PASS1C-06` Only `PASS1C-06`: type `PASS1C-06`
`verbose`	(logical) `TRUE` (default) shows messages