NEWS

RaMS 1.4.3 (2024-10-09)

Added timezone support to metadata's timestamps (mzML files are all UTC afaik)
Fixed several bugs in the README and vignettes (it's been a minute since I recompiled these!)
Switched to canonical CRAN URLs
Handling Suggested packages in the tests more carefully (removed bulk tidyverse call)

Added MS3 support to file reading and minification
- MS3 data is not automatically requested with "everything" (the default) and must instead be added (e.g. grab_what=c("everything", "MS3"))
- msdata$MS3 has an additional column (prepremz) corresponding to the MS1 trigger while the premz now corresponds to the immediately preceding MS2 m/z trigger.
Added option to include polarity as a column per request from MetabolomicsWorkbench
- Enable by setting incl_polarity = TRUE in grabMSdata()
- Not enabled by default to preserve back-compatibility
- Polarity is encoded as 1 for positive mode and -1 for negative mode
Added function to edit the retention times of existing mzML/mzXML files (editMSfileRTs)
- Still feels like it's in development, would love feedback on Github
Swapped out demo files to test incl_polarity and MS3 data
Updated tests and minification vignette to reflect new demo files

Added OpenChrom reading support, credit to @ethanbass for the PR (#18 on Github)
Added several convenience functions and useful documentation for each
- qplotMS1data, a shortcut for the common ggplot2 call
- mz_group(), a way to group raw MS1 data into m/z bins given a ppm error
- trapz(), for integrating RT/intensity data into peak area
Added new vignette with speed & size comparison to other packages and methods
Updated vignettes

Added support for DAD (diode array detection) data with grab_what = "DAD", credit to @ethanbass for the code
Added support for precompiled chromatograms with grab_what = "chroms", credit to @ricardobachertdacunha for the proposal
- Also enables MRM data support per Github issue #6
Squashed some bugs

Added tmzmlMaker, a function that converts mzML and mzXML files to the new tmzML file type
Imported between() and %between% from data.table to avoid the extra library() call every time
Squashed some bugs

Added minifyMSdata, a function that shrinks MS files by excluding masses
Restructured demo files using the new minify* functions to include more useful data
Added prefilter argument to grabMSdata that drops masses below a user-provided intensity threshold
Added quick-start poster to README.md
Added grabAccessionData, a function that extracts arbitrary MS metadata by HUPO-PSI accession number
Squashed some bugs

Enabled rtrange parameter for mzXML files
All retention times are now converted to minutes rather than seconds
Added several vignettes and switched back to knitr for PDF support, abandoning plotly things
- RaMS and friends: some examples of moving data between R and other languages
- Basic integrations: some rudimentary code that can be used to manually integrate peaks
Streamlined README.md

Combined mzML and mzXML handling into one wrapper, grabMSdata, which also handles multiple files simultaneously
Created README.md and included several demos of package functionality
Added several "minified" mzML and mzXML files for demos and examples