QA functions for the MoTrPAC community

validate_proteomics

R Documentation

Validate a Proteomics submissions

Description

Validate a Proteomics submission

Usage

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

Arguments

`input_results_folder`	(char) path to the PROCESSED folder to check
`isPTM`	(logical) `TRUE` if it is Post-Translational-Modification proteomics assay
`cas`	(char) CAS code
`dmaqc_shipping_info`	(char) DMAQC file with shipping information. If not provided (default), then DMQAC validation is not peformed (only done at the BIC)
`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`. However, if this argument is provided, it will take priority (and the phase from the input folder and the `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`
`f_proof`	(char) print out pdf with charts including: Reported Ion Intensity boxplot distribution and percentage of NA values per sample Ratio: ratio boxplot distribution and percentage of NA values per samples
`out_qc_folder`	(char) if f_proof is TRUE, then a folder must be provided
`return_n_issues`	(logical) if `TRUE` (default) 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)
`printPDF`	(logical) if `TRUE` (default print plots to pdf)
`verbose`	(logical) `TRUE` (default) prints QC details.
`check_only_results`	(logical) if `TRUE`, only validates results (default `FALSE`)