Validate a Proteomics submissions

Source: R/proteomics_qc.R

Validate a Proteomics submission

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)

Value

(data.frame) Summary of issues