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

Value

(data.frame) Summary of issues