Changelog • MotrpacBicQC

Critical update validate_refmetname: ensure checking the refmet standarized name. Update refmet tests
Update get_and_validate_mdd()
- Update REST service url
- Update Documentation
- Remove dependency on data.table
Enhance: only one metadata_phase file allowed
Enhance dl_read_gcp: replace data table by read_delim
Enhance open_file: accept only tab delimited files

Critical Update: Resolved an issue where the validation of refmet names was compromised due to updates to the Metabolomics Workbench REST service. This version introduces adjustments to ensure accurate validation of refmet names.

New assays: PROT_OX
Fix package conflicts
OLINK: write release adjustments

Add support for OLINK datasets (check olink_qc vignette to find out more)
Adjust function to download data from GCP (dl_read_gcp): it automatically detects the operating system (arguments ignore_std_err and ignore_std_out deprecated)
Multiple fixes and enhancements

Fix bug preventing the processing of BICRESULTS folders (proteomics)
Make clear that the metadata_phase.txt file is required
Other enhancements

Add 24 hours time support for the acquisition_date (MM/DD/YYYY HH:MM:SS)

Add QC for the new required batching variables
Replace deprecated ggplot function
Fix issues with dl_read_gcp
Other adjustments

Minor adjustments

New tissue codes, abbreviations, and colors available for lateral Gastrocnemius and vena cava

Add new dl_read_gcp
Replace dplyr summarise function (deprecated) by reframe
Fix bug affecting proteomics_plots

Fix typo

Fix bug affecting IMM assays

New metabolomics targeted assays (IMM_GLC, IMM_INS, IMM_CTR)
Remove exception of non-unique raw files allowed for CONV assays, and added to IMM assays
Improve metabolomics documentation

Add exception: unique raw files are now not required for metabolomics CONV assay
Update assay_codes: immunoassay/IMMUNO added. The table now also includes assay hex colours and assay abbreviation

Bug fix

Better handling of large proteomics datasets:
- Proteomics RII plots are skipped if the dataset is too large
- Larger pdf size for proteomics ratio plots
Several improvements and enhancements

Improve DMAQC validation

Update write_proteomics according to latest updates on data/file structure
Fix bugs affecting metabolomics_qc and checks on file_manifest

Metabolomics plots: check if enough compounds to generate plots
Update assay_codes: conventional assays code added (CONV)

Adjustments to generate data releases (deal with pass1a/1c)
Version number will be added to upcoming releases

Update a package’s dependency

Updates affecting the proteomics validation:

validate_proteomics: rename argument run_by_bic to check_only_results. Default is still FALSE (it does not affect CAS)
Adjust size of pdf output depending on the number of samples
Support BICRESULTS_YYYYMMDD folder validation (similar to the currently supported RESULTS_YYYYMMDD and PROCESSED_YYYYMMDD folders). This folder is the output of the proteomics pipeline run by the BIC

Update motrpac color abbreviations

Metabolomics: new density plots
Code optimizations
Bug fixes affecting file manifest checks

Refactor the DMAQC validation. A new file will be required when:
- Two phases are combined in the same batch (e.g., PASS1A-06|PASS1C-06)
- The phase content is different from the input folder name (e.g., PASS1C-06 might be submitted but the input folder name is PASS1A-06)

DMAQC validation: print out missing vial labels
Metabolomics QC: add mz/rt density plots

Improve reporting and handling of required files
Fix minor bugs

Metabolomics: fix manifest checks.

Metabolomics: adjust metabolomic plots to deal with a large number of samples
Metabolomics new plot: sum of intensity/concentration
Metabolomics: detects negative values
Metabolomics: update vignette

Proteomics: support for tmt16
Metabolomics: Improve verbosity for wrong tissue code

Fix bug affecting the validation of refmet_names
Update data objects (immunoassay added)

Refactor the validation of refmet_name. It now checks on at the time using the RefMet API. It also validates multipeak isoforms
The function get_and_validate_mdd() donwload the entire RefMet database (warning, >15MB)
The metabolomics_data_dictionary data object will be soon deprecated.

Support DMAQC validation of human submissions

Adjustments for PASS1C-06
Bug fixes affecting HUMAN phase processing

New Metabolomics QC plots: number and proportion of named vs unnamed features identified

New proteomics QC plots for protein coverage

Bug fix

Update: add human tissue codes

Improved version for checking the file manifest from metabolomics submissions
Enable DMAQC validation for submissions combining multiple phases (e.g. PASS1A-06 + PASS1C-06)

Metabolomics QC: new metabolomics QC plots, including number of IDs per sample, intensity distribution, and percentage of NA values
Markdown: Replace prettydoc by rmdformats
New assay code: CONV (Targeted Conventional metabolites or clinical analytes, provided by Duke)

New Phase: HUMAN (name of the new project folder for the human studies)
Proteomics QC: new proteomics QC plot, number of unique ids per sample
Proteomics QC: improved QC plots

New metabolomics sample_type: QC-ReCAS, Global reference biological material prepared at

Update data dictionary (GTech’s kegg revision)

Bug fixes
Update readme

Proteomics QC: enable option to check data processed at the BIC
Bug fixes (color code)

Proteomics QC: update warnings affecting gene_symbol and entrez_id when missing ids
Fix issue affecting Windows machines (Pierre J-B)
Several Color code fixes * assay (Nicole G)
Bug fixes

New QC checks for the new proteomics requirements

Update metabolomics data dictionary, including:
- Broad Metabolomics revision (39 new kegg ids * minor corrections)
- targeted refmet_name
Fix text in warning in case of missing manifest file
Add and improve tests

Fix and improve check (new required) manifest file for untargeted metabolomics datasets

Update tissue_cols data object (Nicole Gay)

Fix bug in validate_metabolomics affecting unnamed sample check

Improved QC for the required manifest file (proteomics and metabolomics)

Metabolomics data dictionary available as a data object: metabolomics_data_dictionary
The function get_and_validate_mdd() still works, but does not pull the data from Metabolomics Workbench. Just return metabolomics_data_dictionary
Bug fix: the manifest issue count now properly displays the number of issues detected.

Bug fix: restore previous version of bic_animal_tissue_code

Add new assays

Bug fix on DMAQC to deal with missing data in DMAQC table
Proteomics: Address 130C missing channel issue affecting the Broad
Proteomics: add an additional QC check point to validate that all values in vial_label column are unique
Proteomics: write_proteomics updated (only required columns selected)
Fix bugs and typos

Add a check point when expected files are not available in the manifest file

Fix bugs affecting manifest files
Adjustments when files don’t meet requirements

Check new required manifest file in both proteomics and metabolomics submissions
Raw file manifest now optional

Proteomics write proteomics
Proteomics load metabolomics

Proteomics QC support

New assays

Bug fixes