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2008-07-15: 1.13.5
Parallel peak petection using Rmpi
Added mpi.finalize() via .Last
Changed plot.metlin so that x axes is the same on both plots
initialise variables gcc complained about
fix error in searchMetlin method.
xcmsRaw collect changes for simple-er code
added -DWIN32_LEAN_AND_MEAN to Makevars.win to fix ramp build on windows
Fix another windows build issue
Added findPeaksMPI() MPI slave function
moved Rgraphviz from required to suggested packages
Preparations for parallel peak picking using MPI, added xcmsPapply() function
removed duplicate definition of xcmsRaw.getsnScan
helper method added for xcmsRaw.collect
added helper method for collect
export new MS/MS searching methods
Added collect to xcmsRaw to convert to xcmsFragments, for searching
NB findPeaks method doesn't alway pick up all peaks that have ms^n data on them.
Ported phenoData code from 1.13.2
Added MS/MS searching methods. searchMetlin and similarity search methods for MS/MS data.
Added dirty nasty methods to find different metabolotes in metlin XML. the collision energy, name, mode (+/-)
Added MS/MS parser for metlin XML MS/MS data
Fix call to MassSpecWavelet
Reapplied Colins Fix + Michaels changes
enable write.cdf()
Backported mzClust stuff
Fix includeMSn handling in xcmsSet + Graphviz fix + use filepath for CDF path
Restored some (most?) xcmsFragments functionality
2008-06-03: 1.13.4
Ported the following Changes from 1.13.3:
- Migrate to ncdf for xcmsRaw.write()
- Added xcmsRaw CDF export contributed by Peter.Watkins at Food Science Australia (FSA)
- mzClust for spectra alignment
- added method="density/mzClust" to group()
- added methods for MS/MS Database searching and similarity searching
2008-06-03: 1.13.3
Promote stable 1.12.1 to 1.13.3
2008-05-12: 1.12.1
centWave/findmzROI: Fix for CE-MS files
2008-04-30: 1.12.0
BioConductor Release 2.2 version bump
2008-04-29: 1.11.22
Revert yesterdays change, and bring back 1.11.20 with a version bump
to avoid inconsistencies
2008-04-28:
Resurrection of 1.11.18 as 1.11.21
2008-04-18: 1.11.20
Increased "max" parameter of group() from 5 to 50
Fixed : plotTIC won't work if object@tic slot is empty
xcmsSet() now gives an error message if no data files were found
More straightforward API for findPeaks.centWave, much less parameters are needed
CAVE: peak width range (in seconds) is used instead of scale range
CAVE: ppm instead of dev parameter
Added ... to diffreport to pass optional parameters to mt.teststat
Added value = c("into","maxo","intb") parameter to diffreport
Added warning if non-unique scantimes are detected to xcmsRaw()
rawEIC() verifies the scanrange
findPeaks.centWave generates a warning if data seems to be not in centroid mode
Added method isCentroided()
Added prefilter option to findPeaks.centWave
Fixed bug in centWave/fitGauss
Added prefilter option to findmzROI
Speedup for findmzROI
Renamed findMZBoxes to findmzROI
Removed findMZBoxes from NAMESPACE
Fixed plotScan() for "last" spectrum, catch out-of-bounds arguments
2008-04-02: 1.11.19
Import xcms from BioC 2.1
2008-04-02: 1.10.8
Fix duplicate setGeneric() which fails on R-2.7a
Fix BinLinBase which had an uninitialised argument in .Call()
Provide clean base for pulling 1.10.8 into 1.11.19
2008-01-24: 1.10.7
Fix in plot(eic) for xcmsEIC with absent groups
2007-11-13: 1.10.6
Removed unnecessary use of data.frame in findPeaks.centWave(), this fixes
a long delay when large peaklists are generated
2007-11-12: 1.10.5
Increased buffer size in findMZBoxes() to catch a rare bug
2007-11-07: 1.10.4
Standardised peak area calculation by introducing scan-distance multiplier to findPeaks.centWave()
2007-11-07: 1.10.3
Fixed a serious fillPeaks() bug introduced in version 1.9.5, which caused it to
silently fill in zero intensities for almost every missing peak
2007-11-01: 1.10.2
Fixed bug in findPeaks.centWave() buffer initialisation (mzboxes.c)
Added check in findPeaks.matchedFilter() for not picking filter artefacts
2007-10-09: 1.10.1
Added error when xcmsRaw objects are read that have non-monotonic stantimes
Added warning when retcor() is probably overcorrecting
Fixed a bounds checking bug in specPeaks()
2007-10-08: 1.10.0
Bioconductor release 2.1
2007-09-17: 1.9.6
rawEIC uses binary search
findMZBoxes gives proper error messages
findPeaks.centWave
- new baseline and S/N estimation (default snthresh=20)
Bugfix for MSW.getRidge
2007-09-04: 1.9.5
Fixed bug were fillPeaks() would fail if there was <= 1 peak to fill in
Made getPeaks() slightly more memory efficient by correcting an oversight
flush.console() is now called on all systems during long operations
2007-07-16: 1.9.4
Increased buffer size to 100000 in findMZBoxes() to handle also files with a vast number of peaks
Fixed bug in MSW.getRidge() to catch empty ridgeLists
findPeaks.centWave
- The scale on which the peak was localised is also returned
- additional logical argument fitgauss, gaussian fits are no longer mandatory
- Integration method can be choosen: descent on the mexican hat filtered data or on the real data. Method 2 is honest,
while method 1 (default) is more robust to noise.
- runs much faster
2007-06-29: 1.9.3
Added wrapper for MassSpecWavelet peak picking on single spectra (findPeaks.MSW)
Added some more logic to joinOverlappingFeatures()
2007-05-??: 1.9.2
Fixed mzdata problem under windows (ramp.c v1.39 from CVS)
Removed workaround for ramp/gcc bug
2007-05-??: 1.9.1
Workaround for ramp/gcc bug (optimization lowered to -O1 for ramp.c)
Several improvements for findpeaks.centWave
Removed maxGaussErr option in findpeaks.centWave
Fixed bug in joinOverlappingFeatures()
Fixed bug in findpeaks.centWave where rt was not assigned correctly
Updated ramp.c to v1.38 (from CVS)
2007-04-26: 1.8.0 & 1.9.0
introduced namespace
plot(xcmsEIC) problem seems to be fixed
Added :
- rawEIC method
- findMZBoxes method
- findPeaks.centWave method
Modified findPeaks() method to support different findPeaks.* algorithms
RAMP: updated ramp.c (v1.37), ramp.h (from CVS)
- ...
- handle mzData "TimeInSeconds" values
- dealing with mzXML files with missing scans
- support for zlib compression
Check if file exists in xcmsRaw()
Plot (log) colored data points in plotRaw()
Modified findPeaks method:
- Moved column "i" (peak number within combined EIC) to the second-to-last column
- Added column "sn" with signal to noise ratio
xcmsSets now include "i" and "sn" columns in the peaks matrix
Updated Windows NetCDF library to version 3.6.2 (now statically linked into xcms.dll)
Small fixes to xcmsSet generation relating to finding/categorizing files:
- If the files argument is not set, then "./" is no longer appended
- One character directory names, and thus group names, are now supported
Enabled axis labels for OpenGL surface plotting using plotSurf()
Removed formerly depricated function clustunique()
Changed xcmsEIC plotting function from an S4 to an S3 method
2006-04-27: 1.6.1 & 1.7.0
Bioconductor release 1.9 and development branch 2.0
Fixed documentation and DESCRIPTION file for R 2.4.0 package check
2006-08-24: 1.5.2
Fixed bug where xcmsSet() failed if less than 2 peaks were detected in a file
Added warning to xcmsSet() if less than 10 peaks were detected in a file
2006-05-09: 1.5.1
Fixed bug where NetCDF files would have their scans incorrectly reversed
Merged recent changes to RAMP mzXML/mzData parser to support TimeInMinutes
2006-04-27: 1.4.0 & 1.5.0
Bioconductor release 1.8 and development branch 1.9
No changes to code or functionality from 1.3.2
2006-02-25: 1.3.2
Blank spectra in mzXML and mzData files are now ignored
EIC width can now be specified in diffreport()
Better error reporting in getEIC()
Fixed rare problem in getEIC()
2005-12-07: 1.3.1
Added support for reading mzData files
Only full-scan spectra are read from mzXML files
The group() function now returns only unique, non-overalpping peak groups
Replaced clustunique utility function with C implementation: rectUnique
2005-10-14: 1.2.0 & 1.3.0
Bioconductor release 1.7 and development branch 1.8
No changes to code or functionality from 1.1.6
2005-08-26: 1.1.6
Fixed bug in plotPeaks()
Updated for compatibility with R 2.2.0
2005-08-23: 1.1.5
Improved peak identification to return full precision masses
regardless of EIC step size
2005-08-16: 1.1.4
Added mzXML raw data import
Added linear alignment method to retcor()
Added check for too small span in retcor()
Created CHANGELOG
2005-08-11: 1.1.3
Added xcmsEIC class
Added groupNames method to xcmsSet
Fixed bug in EIBPC buffer range calculations
Changed sn argument name to snthresh in findPeaks()
2005-07-21: 1.1.2
Fixed bug in retention time correction leading to NA times
2005-06-22: 1.1.1
Improved xcmsSet() constructor handling of absolute path names
2005-05-20: 1.1.0
Bumped version for Bioconductor 1.7 development cycle
2005-05-11: 1.0.0
Bioconductor 1.6 release
Created workaround for xcmsRaw() slowdown introduced in R 2.1.0
Refined xcmsInstall vignette and plotSurf() function
2005-05-09: 0.5.6
Added xcmsInstall vignette
2005-05-05: 0.5.5
Added check for group data to retcor(), fillPeaks(), & diffreport()
2005-05-04: 0.5.4
Improved plotSurf() function with fixed aspect ratio scaling
Added function documentation
2005-04-28: 0.5.3
Fixed bugs in utility functions
Added function documentation
2005-04-15: 0.5.2
Added options for pruning groups during cross-sample peak matching
Improved dynamic library loading/unloading
2005-04-12: 0.5.1
Fixed warnings during Windows compilation
2005-03-31: 0.5
Checked xcms into Bioconductor SVN repository
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