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)
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