RaMS (development version)
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 1.3.4
- 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 (patch)
- 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
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
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