NEWS

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RaMS 1.4

• 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

RaMS 1.4.0 (2024-03-02)

RaMS 1.3.4 (2023-12-13)

• 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

RaMS 1.3.1 (2022-12-14)

• Squashed a bunch of bugs around CRAN submission
• Changed where unit tests write to
• Improved unit test coverage
• Fixed broken URLs
• Added base64encoding to the package officially

RaMS 1.3.0 (2022-11-28)

DAD and chromatogram handling

• 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

RaMS 1.2.0

The tmzML release

• 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

RaMS 1.1.0

The minification release

• 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

RaMS 1.0.0 (2021-03-22)

The first CRAN release

• 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

RaMS 0.3.0

The documentation update

• Expanded documentation for individual functions, both exposed and unexposed
• Expanded README.md to include simpler demos and link to vignette
• Created vignette to demonstrate the nuances of RaMS
• Created tests to stabilize future package development
• Streamlined example mzML and mzXML files

RaMS 0.2.0

The user-friendly update

• 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

RaMS 0.1.0

The first update

• Defined major functions, constructed package skeleton