v0.4.2

• Add redox processing capability to run_plexedpiper by @TylerSagendorf in #28
• Add more robust checks for read_study_design output.
• Set minimum MSnID version to 1.25.2, though this does not prevent installation of an incorrect version of MSnID from Bioconductor, since the version number on Bioconductor is higher.

Full Changelog: 0.4.1...0.4.2

v0.4.1

• Removed duplicate GENCODE protein IDs from run_plexedpiper output. GENCODE IDs are currently only unique when combining the protein (ENSP) and transcript (ENST) IDs. Since there are so few duplicates, we will remove them rather than concatenating these IDs in the "protein_id" column of the output of make_results_ratio_* and make_rii_peptide_* functions.
• Shortened UniProt headers in run_plexedpiper output to only use the middle portion of the UniProt IDs.
• Bugfix: fixed parsing of crosstab rownames in make_rii_peptide_ph when acetylated peptides also contain PTMs denoted by a "@".
• Requires an update to a version of MSnID built on or after 2023-01-26 when column "unique_id" was added to parse_FASTA_names output.

v0.4.0

• Updated MoTrPAC BIC functions to extract information from GENCODE FASTA headers and include them as columns in results tables.
• Added checks for create_crosstab input.
• Updated run_plexedpiper to accept multiple folder paths. Now capable of integrating multiple datasets with different TMT designs, such as MoTrPAC PASS1A/1C.
• Updated handling of UniProt-to-gene conversion in the make_rii_peptide_* and make_results_ratio_* functions. Now uses gene symbols from FASTA headers and the AnnotationDbi Bioconductor package to convert to Entrez gene IDs, rather than converting from protein to gene symbol and Entrez gene.
• Added "pkgdown" GitHub Action to automatically build website.

❗ This version of PlexedPiper requires a version of MSnID that contains parse_FASTA_names() with the database argument ("uniprot" or "gencode").

v0.3.6

• Added use_mzIdentML argument to read_msgf_data to read mzid files from a local folder.
• Added prefix argument to read_study_design and run_plexedpiper.
• Expanded the functionality of filter_msgf_data to allow for filtering at the SiteID level. This performs the same optimization procedure as when filtering at the peptide level. Also added the filter_msgf_data_SiteID_level wrapper.

v0.3.5

• Added unique_only and refine_prior arguments to run_plexedpiper. Requires an update to a version of MSnID built on or after 2022-04-26, when the refine_prior argument was added to infer_parsimonious_accessions.
• Minor documentation changes.

v0.3.4

• Added the NEWS.md file, which details changes for each release.
• Added the PlexedPiper pkgdown website, which contains pre-built vignettes as well as updates and documentation.

v0.3.3

Added the run_plexedpiper wrapper function, which performs all the steps necessary to go from MS-GF+ and MASIC data to Reporter Ion Intensity (RII) and Ratio Results tables used by the MoTrPAC Bioinformatics Center (BIC).

v0.3.2

It is recommended to reinstall MSnID prior to updating PlexedPiper.

• Added TMT6 and TMT18 tables to reporter_converter.
• Added unit tests for all but the MoTrPAC BIC functions and best_PTM_location_by_Ascore. "test-remap_accessions_uniprot_to_gene_fasta.R" requires a UniProt FASTA file that was recently added to MSnID.
• Stopped running examples if their functions are covered by the unit tests.
• Updated DESCRIPTION: removed unused packages, moved PlexedPiperTestData to suggests to facilitate a lighter installation.
• Removed functions that had previously been migrated to PNNL.DMS.utils during the switch to v0.3.0.
• Reduced computation time and memory usage of filter_msgf_data. This has the added benefit of increasing the precision of the optimization algorithms.
• Added UniProt support to MoTrPAC BIC functions.
• R-CMD-check should no longer produce any errors, warnings, or notes.

v.0.3.1

Removed odbc tools

v.0.3.0

DMS tools were migrated to https://github.com/PNNL-Comp-Mass-Spec/PNNL.DMS.utils.