Changelog
Source:NEWS.md
MSnbase 2.31
MSnbase 2.31.2
- Suggest pRolocdata (>= 1.43.2.1) (that has some extdata, needed to other packages’ vignettes).
MSnbase 2.31.1
- Disable nested parallel processing for
chromatogram()method. - Fix Rd notes.
MSnbase 2.29
MSnbase 2.29.2
- Use fragmentation functions from PSMatch.
- Mention R for Mass Spectrometry in start-up message.
MSnbase 2.29.1
- Check for identical ion header in
readMgfData()(see issue 597).
MSnbase 2.27
MSnbase 2.25
MSnbase 2.25.2
- Fix bug in descendPeaks (see #583)
MSnbase 2.21
Changes in 2.21.7
- Fix mz calculation in
calculateFragmentsfor neutral losses with a charge > 1 (see issue 573).
Changes in 2.21.6
- Allow different orientation of axis labels in image2 (see issue 571).
Changes in 2.21.3
- Fix bug (issue #561).
MSnbase 2.19
Changes in 2.19.2
- Fix
plotwithtype = "XIC"to create an empty plot for samples without data points (issue #549).
MSnbase 2.17
Changes in 2.17.5
- Import quantify generic from ProtGenerics.
- Fix defaults in
calculateFragmentsman page (see issue #537).
Changes in 2.17.4
- Re-implement
impute,MSnSet-methodwithMsCoreUtils::impute_matrix(). - Re-implement
normalise,MSnSet-methodwithMsCoreUtils::normalize_matrix(). - Illustrate
ReporterIonsclass using TMT16. - Re-implement
formatRt()usingMsCoreUtils::formatRt(). - Use
MsCoreUtils::robustSummary()(deleted code in this package). - Use
MsCoreUtils::medianPolish().
Changes in 2.17.3
- Add
normalize,Chromatogrammethod. - Add
filterIntensity,Chromatogrammethod. - Add
align,Chromatogrammethod. - Use two digits when printing retention time seconds
MSnbase 2.15
Changes in 2.15.7
- Fixed some consistency in the processing reporting (contributed by @stanstrup).
Changes in 2.15.6
- Add
extractSpectraDatafunction to extract all data from anMSnExporSpectraobject as aDataFrameto be used with theSpectrapackage.
MSnbase 2.13
Changes in 2.13.9
- Typo in OnDiskMSnExp man page <2020-04-26 Sun>
- Fix plot,[On]MSnExp for centroided data <2020-04-26 Sun>
- Use free x scaling in plot,MSnExp’s facet <2020-04-26 Sun>
Changes in 2.13.7
- Make writeMgfData example runnable <2020-04-20 Mon>
- Fix issue when writing mgf with a connection (PR #505, by Rico Derks) <2020-04-20 Mon>
- Add writeMgfData file/connection unit test <2020-04-20 Mon>
Changes in 2.13.6
- When reading MzTab files, the column names aren’t converted to legal colnames (my make.names) -
check.namesinread.delimis now (internally) set toFALSE. This will make it easier to write MzTab objects back to files. See issue #501 for a discussion. - Re-introduce MzTab write support (contributed by Steffen Neumann). See #502.
Changes in 2.13.5
- Support reading of MzTab-M 2.0 format (contributed by Steffen Neumann).
- Use UTF-8 encoding.
MSnbase 2.11
Changes in 2.11.13
- Fix bug in
readSRMData(issue #486) which caused the function to not discriminate between chromatograms with different precursor collision energy.
Changes in 2.11.12
- Fix bug in
pickPeaks: set variablecentroidedonly toTRUEfor spectra matching the providedmsLevel.. - Add parameter
msLevel.tosmooth.
Changes in 2.11.10
- Updates to
consensusSpectrum: add parametermzFunallowing to define the aggregation function for m/z values, change default formzdto0(hence avoid estimating m/z differences by default) and change the default for parameterintensityFuntomedian.
Changes in 2.11.7
- Add parameter
weightedtoconsensusSpectrumand change the default from reporting the intensity-weighted mean of m/z values for consensus peaks to reporting the m/z of the largest peak <2019-09-12 Thu>.
Changes in 2.11.6
- Update to match changes in mzR version 2.17.4 <2019-09-04 Wed>.
- Add parameter
msLeveltopickPeaksto allow peak picking in specific MS levels. See #478 <2019-09-04 Wed>.
Changes in 2.11.5
- Use
filterMsLevel,filterMz,filterPolarity,filterRt,filterAcquisitionNum,filterEmptySpectra,filterPrecursorScan,productMz,filterPrecursorMzandfilterIsolationWindowgenerics fromProtGenerics`.
Changes in 2.11.4
-
plot,Spectrum,Spectrumnow also supports MS1 spectra (see #477) <2019-07-23 Tue>
Changes in 2.11.3
- Make combineFeatures a method <2019-05-31 Fri>
- Remove message about changed meaning of the “modifications” argument in calculateFragments’ that was introduced in MSnbase 1.17.6 (2015-06-21). <2019-06-01 Sat>
- Implement combineSpectra,MSnExp (see #474) <2019-06-02 Tue>.
MSnbase 2.9
Changes in version 2.9.5
- Add
isolationWindowLowerMzandisolationWindowUpperMzmethods <2019-04-15 Mon> - Add
filterPrecursorMzmethod <2019-04-15 Mon> - Add
filterIsolationWindowmethod <2019-05-16 Tue>
MSnbase 2.7
Changes in version 2.7.11
- Change default for
timeDomainincombineSpectraandcombineSpectraMovingWindowtoFALSE<2018-10-18 Thu> - Add new spectra combination function
consensusSpectrum<2018-10-24 Wed> - Amend plot,Spectrum 1 and 2 (see #369)
Changes in version 2.7.9
- Import rather than depend on BiocParallel <2018-10-15 Mon>
- Fix failing test on Windows (requiring normalizePath) <2018-10-15 Mon>
Changes in version 2.7.7
- Fix unit tests (issue #360, wrong MS OBO CV terms for data smoothing (MS:1000592) and baseline correction (MS:1000593))
Changes in version 2.7.6
- Fix wrong MS OBO CV terms for data smoothing (MS:1000592) and baseline correction (MS:1000593).
Changes in version 2.7.5
- Add a note about parallel processing in vignette (see #356 for background) <2018-09-04 Tue>
Changes in version 2.7.4
- Fix filterMz for spectra with no non-NA intensities in m/z range (see #355) <2018-08-08 Wed>
Changes in version 2.7.3
- Fix bug in robust summary (see PR #349) <2018-07-28 Sat>
- Fix failing unit test <2018-07-28 Sat>
MSnbase 2.5
Changes in version 2.5.14
- Fix changed remote location of mzTab example files <2018-04-19 Thu>
- Fix failing centroided unit test (see issue #338) <2018-04-20 Fri>
Changes in version 2.5.13
- Reduce unit testing time (see #334) <2018-04-13 Fri>
- Fix bug in write.exprs when only one feature data is passed <2018-04-17 Tue>
Changes in version 2.5.12
- Ensure tic and bpi with initial = TRUE calculate the tic and bpi from the data (related to issue #332). <2018-04-10 Tue>
Changes in version 2.5.11
- Improve combineFeatures manual to document the effect for missing values for different types of aggregation methods <2018-04-07 Sat>
- Update robust summary to hangle missing values (see #330). <2018-04-09 Mon>
Changes in version 2.5.10
- New robust summarisation method in
combineFeaturescontributed by Ludger Goeminne, Adriaan Sticker and Lieven Clement <2018-04-03 Tue> - Adapt
utils.removePeaksto newIRangesimplementation; thanks to H. Pagès for the implementation (see PR #320 for discussion) <2018-03-26>. - Centroiding information is retrieved from raw files (for mzML/mzXML files;. see issue #325 <2018-03-27>
- Add parameter
timeDomaintocombineSpectra,combineSpectraMovingWindowandestimateMzScatteringallowing to perform the grouping of m/z values from consecutive scans based on the square root of the m/z values <2018-03-29>. - Assure feature CV feature variable names are unique when combining feature repeatedly (see issue #303) <2018-04-04 Wed>
Changes in version 2.5.9
- New combineSpectra, combineSpectraMovingWindow, estimateMzScattering and estimateMzResulution functions <2018-03-05>.
- New vignette describing profile mode data centroiding <2018-03-05>.
Changes in version 2.5.8
- New as(MSnExp, data.frame) method <2018-02-16>
- Speed up readMgfData function - see issue #319 <2018-03-13 Tue>
Changes in version 2.5.7
- MSmap constructor for OnDiskMSnExp objects (see issue #305) <2018-01-31 Wed>
- New filterMsLevel,MSnSet method <2018-02-06 Tue>
Changes in version 2.5.6
- Fixing processing message when combining two MSnSets (reported by kamal.fartiyal84 https://support.bioconductor.org/p/100865/#105206) <2018-01-24 Wed>
Changes in version 2.5.5
- Added TMT11-plex <2018-01-17 Wed>
- Add
phenoData<-method forpSet(issue #299 <2018-01-22>. - Change readMSnSet2 example <2018-01-23 Tue>
Changes in version 2.5.4
- Add featureData slot to Chromatograms class and add mz, precursorMz and productMz methods for Chromatograms (issue #289) <2017-12-18 Mon>.
- Add readSRMData function to read chromatographic data from SRM (MRM) experiments; issue #286 <2018-01-10 Wed>.
- The MSnSetList class has a new
featureDataslot, accessible withfDatato store metadata for the individial MSnSets of the list.MSnSetListalso not has ansapplymethod. <2018-01-10 Wed> - combineFeatures now has a new
fcolargument (see issue #195) <2018-01-11 Thu>
Changes in version 2.5.3
- Add filterPrecursorScan for
MSnExpandOnDiskMSnExp; closes issue #282 and PR #287 <2017-12-16 Sat>. - MSnSet to/from SummarizedExperiment coercion (contributed by Arne Smits in PR #284) <2017-12-17 Sun>
- Fix inverted M/Z axis in plot3D,MSmap (reported by Sylvain Dechaumet, see issue #292) <2017-12-19 Tue>
Changes in version 2.5.2
- Use automatic backend detection (based on file name and file content) that was introduced in mzR version 2.13.1 (issue #275).
- Fix mzML file writing unit tests to work with recently introduced header column “filterString” (issue #278).
- Reduce number of comparsions in in internal
fastquant_maxto get little speed improvents for isobaric quantification (see PR #280) <2017-11-27 Mon>. - MIAxE, MSnProcess and AnnotatedDataFrame coercion to list methods (in related to PR #280) <2017-12-11 Mon>
- Add support to reduce the featureData for OnDiskMSnExp objects (issue #285) <2017-12-11 Mon>.
Changes in version 2.5.1
- Update dependencies (see issue #271)
- Replace HCD by ETD in TMT10ETD’s name/description
MSnbase 2.3
Changes in version 2.3.13
- Add write support for MSnExp and OnDiskMSnExp objects allowing to save the MS data to mzML or mzXML files. <2017-09-15 Fri>
Changes in version 2.3.12
- Keep
protocolDatain isobaric quantification; fixes #265
Changes in version 2.3.10
- New
isCentroidedFromFilefunction <2017-08-11 Fri> - Add msLevel slot to Chromatogram object <2017-08-16 Wed>
- Add msLevel argument to chromatogram,MSnExp method <2017-08-16 Wed>
-
calculateFragmentsnow just calculate fragments for alln - 1Lbonds (before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun> - Add
isEmptymethods forChromatogramandChromatogramsobjects <2017-09-05 Tue> - plot,Chromatogram[s] creates an empty plot and returns a warning if the Chromatogram[s] object is empty (issue #249) <2017-09-05 Tue>
Changes in version 2.3.9
- Using new mzR::openIdfile backend to add identifcation data to raw and quantitative data (see issue #232) <2017-07-28 Fri>
- New utils functions: factorsAsStrings, makeCamelCase and reduce,data.frame <2017-07-29 Sat>
- Coerce mzRident to data.frames <2017-07-29 Sat>
- Add phenoData slot to Chromatograms class<2017-08-02 Wed>
- new readMzIdData function to read mzId files as data.frames (uses the new coerce,mzRident,data.frame method) <2017-08-03 Thu>
- new filterIdentificationDataFrame function to filter PSM data.frames as produced by readMzIdData. Also used in the addIdentificationData methods. <2017-08-03 Thu>
- readMSData has a new mode argument to set onDisk or inMemory (default) mode <2017-08-10 Thu>
Changes in version 2.3.6
- Brutally remove xic and chromatogram functions/methods, to be replaced by the Chromatogram[s] infrastructure <2017-06-15 Thu>
Changes in version 2.3.4
- Use the injection time from mzR (see PR #109) which in now in seconds (was in milliseconds) <2017-06-13 Tue>
Changes in version 2.3.3
- Rewrite
getColsFromPatternandgetRowsFromPatternand add unit tests <2017-05-11 Thu>. - Add
.filterNAand rewritefilterNAformatrixandMSnSet<2017-05-11 Thu>. - Convert main MSnbase-demo vignette to Rmd/html <2017-05-27 Sat>
-
naplotgains areorderRowsandreorderColumnsargument <2017-06-05 Mon>.
Changes in version 2.3.2
- Rewrite
utils.clean. It now keeps just the zeros in the direct neighbourhood (see #210) <2017-05-04 Thu>.
MSnbase 2.1
Changes in version 2.1.19
- Set SerialParams() in an attempt to avoid random errors in tests - see issue #205 <2017-04-24 Mon>
Changes in version 2.1.16
- Remove timing test as it fails occasionally on the Bioconductor servers <2017-04-09 Sun>
Changes in version 2.1.15
- Remove reshape2 dependency; see #201 <2017-04-06 Thu>
Changes in version 2.1.14
- Internal rewrite and speedup of topN; Briefly multiple apply calls are avoided,
getTopIdxandsubsetByIdare replaced by.topIdx. See PR #199 for details. <2017-03-20 Mon> - Fix mz calculation for terminal modifications and z > 1 in
calculateFragments; closes #200 <2017-03-22 Wed> - Fix errors and notes <2017-03-30 Thu>
Changes in version 2.1.12
- Import dist from stats <2017-02-25 Sat>
- Fix filing example <2017-02-25 Sat>
Changes in version 2.1.10
- New
diff.mediannormalisation forMSnSets. <2017-01-26 Thu> - Fix combineFeatures message <2017-02-01 Wed>
Changes in version 2.1.9
- When fully trimmed, an (empty) spectrum has peaksCount of 0L - see https://github.com/https://github.com/lgatto/MSnbase/issues/184 <2017-01-20 Fri>
- Add filterEmptySpectra,MSnExp method (see issue #181) <2017-01-20 Fri>
- Add a section about notable on-disk and in-memory differences (was issue #165) <2017-01-20 Fri>
Changes in version 2.1.8
- Remove order option altogether <2017-01-19 Thu> (superseeds setting default sorting using “auto” on R < 3.3 and “radix” otherwise <2017-01-03 Tue>)
Changes in version 2.1.7
- Setting default sorting using “auto” on R < 3.3 and “radix” otherwise <2017-01-03 Tue>
- filterMz returns an empty spectrum when no data is within the mz range (see issue #181) <2017-01-16 Mon>
- Performance improvement: a new private .firstMsLevel will efficiently return the first MS level in an MSnExp and OnDiskMSnExp. See issue #183 for details/background <2017-01-18 Wed>
Changes in version 2.1.6
- Migrate io and dev vignettes to BiocStyle’s html_document2 style <2016-12-23 Fri>
- Update show method to display class.
- Migrated to NEWS.md <2016-12-23 Fri>
- Update DESCRIPTION (and README) to reflect wider usage of MSnbase (replaced MS-based proteomics by mass spectrometry and proteomics) <2016-12-23 Fri>
Changes in version 2.1.3
- FeaturesOfInterest collections can now be assigned names - addresses issue #172 <2016-11-25 Fri>
Changes in version 2.1.2
- Update readMSnSet2 to save filename <2016-11-09 Wed>
- Ensure that header information is read too if spectra data is loaded for onDiskMSnExp objects (see issue #170) <2016-11-24 Thu>
MSnbase 1.99
Changes in version 1.99.5
- Add removeReporters,OnDiskMSnExp (see issue #161 for details) <2016-10-07 Fri>
Changes in version 1.99.3
- Injection time is now added to the header when reading mzML files using readMSData2 (see issue #159) <2016-10-04 Tue>
Changes in version 1.99.2
- Added isolationWindow,MSnExp method <2016-09-23 Fri>
- Updated readMSData Spectrum2 class to support MS levels > 2 <2016-09-30 Fri>
Changes in version 1.99.1
- Fix MS level test in quantify,OnDiskMSnExp to support MS2+ level quantitation <2016-09-14 Wed>
Changes in version 1.99.0
- Add normalize method for onDiskMSnExp <2016-06-07 Tue>.
- Fix bug in readMSData <2016-06-07 Tue>.
- Added documentation and unit test for trimMz <2016-06-01 Wed>.
- Added trimMz method for onDiskMSnExp objects <2016-05-31 Tue>.
- Added (internal) method spectrapply to apply a function to all spectra of an onDiskMSnExp object; does the data import, subsetting, application of lazy processing steps etc. <2016-05-27 Fri>.
- Added a section to the MSnbase-development vignette <2016-05-27 Fri>.
- Finished with all pSet inherited methods and docs <2016-05-26 Thu>.
- Added rtlim argument to spectra method for onDiskMSnExp <2016-05-26 Thu>.
- Methods rtime, tic, ionCount, polarity and acquisitionNum implemented <2016-05-25 Wed>.
- Documentation added for most methods <2016-05-25 Wed>.
- Methods peaksCount and spectra for onDiskMSnExp objects implemented <2016-05-24 Tue>.
- Performance and validation tests for the Spectrum1 C-constructor <2016-05-23 Mon>.
- Spectrum1 constructor implemented in C (presently not exported) <2016-05-20>
- length, scanIndex, acquisitionNum and centroided implemented <2016-05-20>
- Implemented fromFile and msLevel for onDiskMSnExp <2016-05-19 Thu>
- Implemented an onDiskMSnExp class for on-the-fly data import <2016-05-19 Thu>
- Fixed the validate method for pSet to play nicely with onDiskMSnExp objects <2016-05-19 Thu>
- Added slot onDisk to pSet objects (TRUE for onDiskMSnExp objects, FALSE otherwise). The getter method isOnDisk checks for the presence of the slot in the object (backward compatibility) <2016-05-19 Thu>
- Implemented a ProcessingStep class that helps to keep track how (spectra) data should be processed on the fly <2016-05-18 Wed>
- In onDiskMSnExp validity, check that the assaydata is empty <2016-06-28 Tue>
- Pass neutralLoss in plot,Spectrum,Spectrum-method to .calculateFragments; fixes #146 <2016-08-12 Fri>
- Allow the user to specify the
cex,lwd,pchfor peaks and fragments in plot,Spectrum,Spectrum-method; closes #148 <2016-08-12 Fri> - Update centroided with an na.fail argument (see issue #150 for details) <2016-08-12 Fri>
- Fix warning in readMgfData if TITLE contains multiple “=” <2016-08-24 Wed>
MSnbase 1.21
Changes in version 1.21.8
- Update MSnSet validity method to guard agains empty string feature names <2016-06-20 Mon>
- Simplify show,MSnExp method to work for various MS level cases and onDiskMSnExp - addressed issue #98 <2016-06-28 Tue>
- removeMultipleAssignment also removes features that were not assigned (i.e. that have fcol (nprots) NA) <2016-07-02 Sat>
- New smoothed slot/accessor/replacement methods <2016-07-08 Fri>
- Update reporter masses and add TMT10 ETD/HCD <2016-07-20 Wed>
- returning empty spectrum when fliterMz has empty range - see issue #134 <2016-07-22 Fri>
- (mz, intensity) values are reordered based on order(mz) - see issue #135 <2016-07-26 Tue>
- fix bug in bin,Spectrum - see issue #137 <2016-08-05 Fri>
Changes in version 1.21.7
- Update iPQF reference <2016-06-01 Wed>
- Fix a bug in normalize method for MSnExp objects: assigning normalized spectra directly to assayData is not possible, as the environment is locked. See PR #91.
- readMSData: if no phenodata is provided it creates an empty one with rownames corresponding to the file names. See PR #91.
- Lock itraqdata’s assaydata bindings <2016-06-08 Wed>
Changes in version 1.21.6
- MSmap unit test <2016-05-23 Mon>
- Fix bug in as(MSmap, “data.frame”) <2016-05-23 Mon>
Changes in version 1.21.5
- Added Johannes as contributor <2016-05-12 Thu>
- Deprecate MzTab v0.9 <2016-05-19 Thu>
- Fix old googlecode URLs to old MzTab <2016-05-19 Thu>
Changes in version 1.21.4
- More MzTab and Spectrum1 unit testing <2016-05-08 Sun>
- Speed up readMSData (PR #86 by jotsetung) <2016-05-12 Thu>
- Replace example file URL to use github instead of googlecode <2016-05-12 Thu>
Changes in version 1.21.3
- No fileNames replacement method <2016-05-07 Sat>
- fileNames unit tests <2016-05-07 Sat>
- add fileNames to class that had fileName accessor (MSmap, MzTab) <2016-05-07 Sat>
Changes in version 1.21.1
- Fix wrong indexing in readMSdata, msLevel==1 (PR #85 by jotsetung) <2016-05-04 Wed>
- grep/getEcols have a ‘n’ param specifying which line to grep/get <2016-05-04 Wed>
MSnbase 1.19
Changes in version 1.19.22
- more unit tests <2016-04-23 Sat> <2016-04-24 Sun> <2016-04-26 Tue>
- remove readIspyData functions <2016-04-23 Sat>
- Fixed bug in error catching in utils.mergeSpectraAndIdentificationData <2016-04-23 Sat>
Changes in version 1.19.19
- new naplot function to visualise missing values as a heatmap and barplots along the samples and features. <2016-04-04 Mon>
Changes in version 1.19.17
- Write support of mzTab has been dropped (writeMzTabData, makeMTD, makePEP and makePRT are now defunct) <2016-03-18 Fri>
Changes in version 1.19.16
- add estimateNoise,[Spectrum|MSnExp]-method; closes #78 <2016-03-10>
- import a lot of functions from recommended packages, namely graphics, stats and utils to avoid many “Undefined global functions or variables” NOTEs in R CMD check <2016-03-10>
Changes in version 1.19.15
- limit readMSData unit test due to Windows-only error <2016-03-09 Wed>
- fix unit test for utils.colSd(x, na.rm=TRUE)
Changes in version 1.19.13
- Fixed bug in bin_Spectrum, reported by Weibo Xie <2016-02-16 Tue>
- Added unit test for bug above <2016-02-16 Tue>
- Merged ‘apply functions columnwise by group’ <2016-02-16 Tue>
- In nQuants, the fcol argument has been replaced with groupBy to make the signature consistent with featureCV <2016-02-16 Tue>
Changes in version 1.19.12
- Moved polarity slot from Spectrum1 (0.1.0 -> 0.2.0) to Spectrum (0.2.0 -> 0.3.0) superclass; also bumped Spectrum2 class (0.1.0 -> 0.2.0) and MSnExp (0.3.0 -> 0.3.1, to trace changes in Spectrum2). Wrote MSnExp and Spectrum2 updateObject methods. <2016-02-11 Thu>
Changes in version 1.19.11
- Fix trimws generic/methods with useAsDefault (see issue #75) <2016-02-02 Tue>
- add exprs,MSnSet-method alias (since exprs is now exported) <2016-02-02 Tue>
Changes in version 1.19.8
- readMSnSet2 now also accepts a data.frame as input <2016-01-29 Fri>
- selective ggplot2 import <2016-01-29 Fri>
Changes in version 1.19.7
- new sampleNames<- for pSet and MSnExp objects <2015-12-15 Tue>
- Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat) <2015-12-18 Fri>
Changes in version 1.19.6
- MSnExp feautreNames are now X01, X02 (0 after X) to maintain numerical sorting of ASCII characters; contributed by sgibb <2015-12-14 Mon>
- Update MSnbase:::subsetBy to use split instead of lapply, which makes topN faster. This nevertheless changes the order of the resulting MSnSet (see issue #63 for details and background); contributed by sgibb <2015-12-14 Mon>
Changes in version 1.19.5
- Merged pull request #67 from lgatto/featureCV by sgibb: featureCV ignores its na.rm argument <2015-12-12 Sat>
Changes in version 1.19.3
- New argument fcol to selectFeatureData to select feature variables using a vector <2015-10-28 Wed>
MSnbase 1.17
Changes in version 1.17.16
- new default parameter ‘feature weight’ in iPQF by Martina Fisher (see PR#65) <2015-10-07 Wed>
Changes in version 1.17.13
- partly rewrite writeMgfData <2015-05-16 Thu>
- initial hmap function <2015-07-16 Thu>
- fix bug in plotting MS1 spectra (closes issue #59) <2015-07-16 Thu>
- new image implementation, based on @vladpetyuk’s vp.misc::image_msnset <2015-07-25 Sat>
- Changed the deprecated warning to a message when reading MzTab data version 0.9, as using the old reader can not only be achived by accident and will be kept for backwards file format compatibility <2015-07-30 Thu>
Changes in version 1.17.11
- adding unit tests <2015-07-01 Wed>
- fix abundance column selection when creating MSnSet form MzTab <2015-07-01 Wed>
- new mzTabMode and mzTabType shortcut accessors for mode and type of an mzTab data <2015-07-01 Wed>
Changes in version 1.17.8
- coercion from IBSpectra to MSnSet, as per user request <2015-06-23 Tue>
- new iPQF combineFeature method <2015-06-24 Wed>
Changes in version 1.17.6
- Export metadata,MzTab-method <2015-06-19 Fri>
- Replace spectra,MzTab-method by psms,MzTab-method <2015-06-20 Sat>
- Change the meaning of calculateFragments’ “modifications” argument. Now the modification is added to the mass of the amino acid/peptide. Before it was replaced. <2015-06-21 Sun>
- calculateFragments gains the feature to handle N-/C-terminal modifications, see #47. <2015-06-21 Sun>
- update readMzTabData example <2015-06-22 Mon>
Changes in version 1.17.5
- new MzTab class to store a simple parsing of an mzTab version 1 data file. See ?MzTab for details. <2015-06-16 Tue>
Changes in version 1.17.4
- New lengths method for FoICollection instances <2015-06-06 Sat>
- New image2 function for matrix object, that behaves like the method for MSnSets <2015-06-10 Wed>
- image,MSnSet labels x and y axis as Samples and Features <2015-06-10 Wed>
- fixed bug in purityCorrect, reported by Dario Strbenac <2015-06-11 Thu>
MSnbase 1.15
Changes in version 1.15.18
- fix failing test_MSnExp::readMSData unit test on Windows i386 (@.cache$size being different on that arch) [2015-04-14 Tue]
- merge @vladpetyuk PR #50 fix of combine features bug [2015-04-14 Tue]
Changes in version 1.15.15
- using serial parallelisation during quantitation in unit tests [2015-04-02 Thu]
Changes in version 1.15.14
- new msnset data, used in various examples instead of quantifying the itraqdata experiment over and over again [2015-04-01 Wed]
Changes in version 1.15.13
- improve nbavg imputation description and add example [2015-03-22 Sun]
- reduce compareSpectra example timing [2015-03-30 Mon]
Changes in version 1.15.12
- average neighbour imputation for ordered fractions along a gradient [2015-03-21 Sat]
Changes in version 1.15.10
- update compareSpectra man [2015-03-19 Thu]
- ExpressionSet <-> MSnSet coercion [2015-03-19 Thu]
Changes in version 1.15.7
- Importing ProtGenerics [2015-02-28 Sat]
- selective import of MALDIquant [2015-03-02 Mon]
Changes in version 1.15.6
- add intensity column to the calculateFragments output; closes #47;1 [2015-02-02 Mon]
- add method argument to calculateFragments to allow the user choosing the highest/closest peak or all peaks in the tolerance range; closes #47;2 [2015-02-09 Mon]
- add neutralLoss argument to calculateFragments and calculate loss of water and ammonia; closes #47:3 [2015-02-19 Thu]
- new imputation methods via imputeLCMD and norm [2015-02-09 Mon]
- vignette updates [2015-02-09 Mon]
- imputation unit test [2015-02-24 Tue]
Changes in version 1.15.5
- update dependency to mzID >= 1.5.2 [2015-01-28 Wed]
- rewrite addIdentificationData and change its signature [2015-01-28 Wed]
- add methods addIdentificationData which work on MSnExp and MSnSets using filenames (characters), mzID objects and data.frames; see #42; closes #45; [2015-01-28 Wed]
- add a section about MSmaps in the vignette [2015-02-02 Mon]
- MSmap has a new zeroIsNA argument to set all 0 values of the map to NA. This simplifies the resulting plot3D figure. [2015-02-02 Mon]
Changes in version 1.15.4
- partly rewrite readMgfData [2015-01-19 Mon]
- Typo in addIdentification data man [2015-01-20 Tue]
- use Biocstyle [2015-01-23 Fri]
- replace require with requireNamespace [2015-01-23 Fri]
Changes in version 1.15.3
- plot,Spectrum2,character to add fragment ions based on peptide sequence [2014-11-20 Thu]
- update vignette with above [2014-11-20 Thu]
- comment parallel code in quantify man [2015-01-09 Fri]
Changes in version 1.15.2
- merged sgibb’s pull request exporting overloaded methods as well [2014-11-02 Sun]
- updated MSnSet validity, checking that exprs(.) is a matrix [2014-11-12 Wed]
- fix error (missing header extraction) is MSmap example [2014-11-18 Tue]
Changes in version 1.15.1
- Fixing error when id file has no spectrumFile info (see issue #39) and return a warning (instead of an error) when the file used to create the MSnExp/MSnSet and mzid file were different [2014-10-15 Wed]
MSnbase 1.13
Changes in version 1.13.16
- width generic if non-existant [2014-09-03 Wed]
- fix undocumented S4 methods warnings [2014-09-27 Sat]
Changes in version 1.13.15
- msMap(MSmap)<- method [2014-08-12 Tue]
- Typo in MIAPE man [2014-08-29 Fri]
Changes in version 1.13.14
- Fix xic example [2014-08-08 Fri]
- importing lattice, ggplot2 (was depends) and suggesting rgl [2014-08-09 Sat]
- MSmap infrastructure [2014-08-09 Sat]
Changes in version 1.13.12
- Don’t import width from IRanges [2014-07-23 Wed]
- qual slot is populated again [2014-07-23 Wed]
Changes in version 1.13.10
- new averageMSnSet function to generate an average over a list of MSnSets. [2014-06-17 Tue]
- new non-parametric coefficent of variation function [2014-06-17 Tue]
- Using/importing IRanges::width [2014-06-18 Wed]
Changes in version 1.13.9
- new listOf helper function [2014-06-16 Mon]
- compfnames to compare and document differences in MSnSet feature names [2014-06-16 Mon]
- suggesting Vennerable (compfnames example) and roxygen2 (generate rd) [2014-06-16 Mon]
Changes in version 1.13.6
- new isEmpty method for Spectrum instances [2014-05-14 Wed]
- removePeaks does not try for empty Spectra [2014-05-14 Wed]
- isEmpty unit test [2014-05-14 Wed]
Changes in version 1.13.5
- export .get.amino.acids function [2014-05-08 Thu]
- removePeaks for centroided data [2014-05-08 Thu]
- add new exported function get.atomic.mass [2014-05-08 Thu]
- Spectrum[2] prototype sets centroided=FALSE by default (instead of logical()) [2014-05-08 Thu]
- fnamesIn also supports y = “data.frame” [2014-05-14 Wed]
- Using BiocParallel for parallel support; replaced parallel argument with BPPARAM [2014-05-14 Wed]
Changes in version 1.13.4
- Document difference between traceable and non-traceable FeaturesOfInterest instances [2014-04-30 Wed]
- ignoring desciptions with length > 1 [2014-04-30 Wed]
Changes in version 1.13.2
- add compareSpectra to compare Spectrum objects [2014-04-09 Wed]
- add bin method for Spectrum objects [2014-04-09 Wed]
- recreate inst/extdata/msx.rda for R 3.1 and Biobase 2.24 [2014-04-13 Sun]
- add plot,Spectrum,Spectrum method [2014-04-14 Mon]
- add calculateFragments,character,Spectrum and calculateFragments,character,missing methods [2014-04-15 Tue]
- updated readMSData test unit to ignore object@.__classVersion__ that fails with latest R/Bioc versions [2014-04-15 Tue]
- formatRt conversion from ‘mm:sec’ to sec and unit test [2014-04-17 Thu]
- Update nprot/npsm.prot/npsm.pep/npep.prot feature variables and relevant man/tests/argument defaults [2014-04-17 Thu]
MSnbase 1.11
Changes in version 1.11.13
- Document [get|grep]Ecols in io vignette [2014-03-31 Mon]
- typo in readMSnSet man [2014-03-31 Mon]
- updated affiliation in vignettes [2014-03-31 Mon]
Changes in version 1.11.12
- Fixed a bug in readMzTabData reported by Hendrik Weisser [2014-03-26 Wed]
Changes in version 1.11.11
- precomputed msx test data now has id data [2014-03-25 Tue]
- quantitation unit tests [2014-03-25 Tue]
- quantify method now accepts label-free methods [2014-03-25 Tue]
Changes in version 1.11.10
- import mzID [2014-03-20 Thu]
- dummyiTRAQ id extdata [2014-03-21 Fri]
- add addIdentificationData method for MSnExp and MSnSet [2014-03-21 Fri]
- using data from pRolocdata (was pRoloc) [2014-03-23 Sun]
- added removeNoId,MSnExp,MSnSet methods [2014-03-23 Sun]
- added idSummary,MSnExp,MSnSet methods [2014-03-24 Mon]
- Not generating different sample per file when reading raw data. pData(.) now has systematically 1 row if not specifically provided by the user. A message is also reported by validity,pSet if row(pData(.)) > 1. [2014-03-24 Mon]
- NAnnotatedDataFrame now has default multiplex 1 [2014-03-25 Tue]
- NAnnotatedDataFrame unit tests [2014-03-25 Tue]
Changes in version 1.11.9
- write.exprs can have fDataCol or fcol (for consistence) [2014-03-17 Mon]
- Fixing bug in combineFeatures(…, is.character(groupBy)) [2014-03-19 Wed]
- fixed combineFeatures [2014-03-20 Thu]
- added example, test and doc for combineFeatures with list [2014-03-20 Thu]
Changes in version 1.11.8
- adding redundancy handling to combineFeatures (by vladpetyuk, pull request #18) [2014-03-14 Fri]
- updated combineFeatures signature to accomodate above changes [2014-03-14 Fri]
- updated unit tests for new testhat 0.8 [2014-03-14 Fri]
Changes in version 1.11.6
- add corresponding xcms functions to the chromatogram and xic manual page [2014-02-21 Fri]
- new bpca imputation methods [2014-02-27 Thu]
- replacing stop_on_error with option in vignette [2014-02-27 Thu]
Changes in version 1.11.5
- typo in MSnSet droplevels man [2014-01-27 Mon]
- typo in MSnbase-demo vignette [2014-02-20 Thu]
- fix BPI legend in chromatogram [2014-02-20 Thu]
Changes in version 1.11.4
- passing … to sweep when normalising [2013-12-08 Sun]
- updated makeMTD to accomodate new MS ontology [2013-12-23 Mon]
MSnbase 1.9
Changes in version 1.9.12
- fix MSnSet -] ExpressionSet [2013-10-13 Sun]
- MSnSet -] ExpressionSet unit test [2013-10-13 Sun]
Changes in version 1.9.11
- MIAPE to MIAME conversion [2013-10-11 Fri]
- proper MIAME when MSnSet -] ExpressionSet [2013-10-11 Fri]
Changes in version 1.9.10
- faster plotMzDelta [2013-09-28 Sat]
- faster plotMzDelta for mzRramp instances [2013-09-29 Sun]
- chromatogram method [2013-10-04 Fri]
- plotMzDelta has subset arg [2013-10-04 Fri]
- xic method [2013-10-04 Fri]
- suggesting msdata for chromatogram example [2013-10-04 Fri]
- renamed plotting arg ‘centroided.’ [2013-10-04 Fri]
Changes in version 1.9.9
- typo in filterNA Rd [2013-09-18 Wed]
- writeMgfData now has a progress bar [2013-09-24 Tue]
- centroided(MSnExp) <- TRUE now allowed [2013-09-24 Tue]
Changes in version 1.9.8
- using new.env(parent=emptyenv()) to get rid of enclosing env when creating new MSnExps [2013-09-17 Tue]
- new (private) MSnExp.size function [2013-09-17 Tue]
Changes in version 1.9.7
- Passing … to read.table in MSnbase:::readIspy[Silac|15N]Data [2013-09-16 Mon]
- QualityControl biocView [2013-09-16 Mon]
Changes in version 1.9.6
- new as.data.frame.MSnSet method [2013-08-16 Fri]
- new ms2df function [2013-08-16 Fri]
- new getEcols and grepEcols helpers for readMSnSet2 [2013-08-16 Fri]
Changes in version 1.9.3
- Using knitr as VignetteEngine [2013-04-29 Mon]
- Remove LazyLoad from DESCRIPTION, which is default nowadays [2013-04-29 Mon]
- knitr dependency ] 1.1.0 for VignetteBuilder [2013-04-29 Mon]
- Adding MSnSet creating sections in io vignette [2013-04-29 Mon]
- new readMSnSet2 function [2013-04-30 Tue]
Changes in version 1.9.2
- clean has now a all param (default FALSE is retain original behavious) to remove all 0 intensity values [2013-04-17 Wed]
- using BiocGenerics::normalize [2013-04-25 Thu]
MSnbase 1.7
Changes in version 1.7.25
- updated itraqdata to fix issue in vignette when combine(exp1, exp2) and different MIAPE versions [2013-03-22 Fri]
Changes in version 1.7.24
- Mention scale in vignette [2013-03-02 Sat]
- exprsToRatio matrix method [2013-03-20 Wed]
Changes in version 1.7.23
- new private nologging function [2013-02-21 Thu]
- adding total number of features on plotNA [2013-02-22 Fri]
- updated msnbase.r [2013-02-26 Tue]
Changes in version 1.7.20
- Explicitating that normalise and normalize are the same methods in the man. [2013-02-13 Wed]
Changes in version 1.7.19
- adding MIAPE and pSet accessors: analyserDetails, analyzerDetails, ionSourceDetails, instrumentModel, instrumentManufacturer, instrumentCustomisations [2013-02-12 Tue]
- switching back to analyserDetails slot [2013-02-12 Tue]
Changes in version 1.7.18
- readMgfData now supports comments and PEPMASS with precursor mz and intensity, requested by Thomas Taus [2013-02-11 Mon]
- improved and running read/writeMgfData example [2013-02-11 Mon]
- new scanIndex accessor method [2013-02-11 Mon]
Changes in version 1.7.17
- added a analyzer accessors/slot to accomodate new mzTab files with more meta-data [2013-01-30 Wed]
Changes in version 1.7.15
- new scale method [2013-01-11 Fri]
- renaming scale.mean and scale.median normalisation methods to center.mean and centre.median [2013-01-11 Fri]
Changes in version 1.7.14
- new unexported readIspy15NData [2013-01-09 Wed]
- min.int readIspy[Silac|15N]Data arg [2013-01-11 Fri]
Changes in version 1.7.13
- msnbase.r v0.1.1 with oh (help) arg [2013-01-08 Tue]
- msnbase.r coerce ob arg to numeric [2013-01-08 Tue]
- testing if any features left in readIspyData [2013-01-08 Tue]
Changes in version 1.7.12
- updated makeImpuritiesMatrix to create matrix from csv file with correction factors [2012-12-23 Sun]
- makeImpuritiesMatrix test [2012-12-23 Sun]
- readIspyData: message instead of warning if NA in featureData [2012-12-24 Mon]
- Added msnbase.r script [2012-12-24 Mon]
Changes in version 1.7.11
- new ‘pattern’ argument to filterNA [2012-12-15 Sat]
- vignette and man updates [2012-12-15 Sat]
- filterNA(, pattern) tests [2012-12-15 Sat]
Changes in version 1.7.10
- new droplevels.MSnSet S3 method [2012-12-14 Fri]
- fixed errors in vignette and udpates [2012-12-14 Fri]
- vignette build stops in case of error [2012-12-14 Fri]
Changes in version 1.7.9
- Updating processing data on readIspyData [2012-12-05 Wed]
- filterNA has a droplevels arg [2012-12-05 Wed]
- featureCV’s default cv.norm is ‘sum’ now [2012-12-11 Tue]
- fixed featureCV for 1 sample [2012-12-11 Tue]
Changes in version 1.7.8
- new featureCV function [2012-12-04 Tue]
- more MSnSet combineFeatures tests [2012-12-04 Tue]
- new TMT6 impurity matrix and fixed purityCorrect [2012-12-05 Wed]
- combineFeatures now automatically computes feature CVs (using featureCV) and collates this in featureData [2012-12-05 Wed]
- new exprsToRatios method (moved from pRoloc) [2012-12-05 Wed]
- initial implementation of impurity correction using Cramer’s rule (see MSnbase:::cramer4) [2012-12-05 Wed]
Changes in version 1.7.7
- added scale.mean and scale.median MSnSet normalisation method [2012-11-30 Fri]
- improvements to readMSData [2012-11-30 Fri]
- small updates to caching code, max level 2 [2012-11-30 Fri]
- readMSdata test [2012-12-01 Sat]
Changes in version 1.7.5
- dropping levels in readIspySilacData [2012-11-06 Tue]
- fixed plotNA [2012-11-09 Fri]
Changes in version 1.7.4
- exporting log method [2012-11-02 Fri]
- private readIspySilacData function [2012-11-05 Mon]
- updating ‘[’-MSnSet to log intial/final dims [2012-11-05 Mon]
MSnbase 1.5
Changes in version 1.5.25
- fixed bug when quantifying exp of length 1 (reported by Colin Archer), added test [2012-09-26 Wed]
- fixed parallel default to FALSE [2012-09-26 Wed]
Changes in version 1.5.24
- updated clean, removePeaks, combineFeatures, purityCorrect, trimMz, plot, MSnSet-class examples to not use readMSData [2012-09-25 Tue]
- fixed clean,MSnExp-method [2012-09-25 Tue]
- space in log message in extractPrecSpectra [2012-09-25 Tue]
Changes in version 1.5.23
- updated quantify documentation [2012-09-24 Mon]
- changed all foo.class functions to foo_class [2012-09-24 Mon]
Changes in version 1.5.22
- setting parallel default to FALSE [2012-09-22 Sat]
- enhanced parallel in DESCRIPTION and detectCores() passed to registerDoMC [2012-09-23 Sun]
Changes in version 1.5.21
- removed registerDoMC no visible global function NOTE [2012-09-21 Fri]
- fixed NOTE about xvarname which was a bug [2012-09-21 Fri]
Changes in version 1.5.20
- an immediate warning is thrown is any(centroided(object)) in quantify.MSnExp [2012-09-15 Sat]
- mzTab file and loading time is now recorded in processingData [2012-09-15 Sat]
- temporarily dontrun’ing’ the mzTab read/write examples as -LS is down (and breaks rols) (note: modifed Rd files, not roxygen template) [2012-09-15 Sat]
Changes in version 1.5.19
- updated all ReporterIons rda data [2012-09-13 Thu]
- Using && in testing parallel, require(foreach and doMC) [2012-09-14 Fri]
Changes in version 1.5.18
- new log method for MSnSet instances [2012-09-13 Thu]
- new MAplot methods using generic and ma.plot/mva.pairs from affy [2012-09-13 Thu]
Changes in version 1.5.17
- changed TMT7[7] mass from 229.26 to 230.17 and ReporterIons descriptions [2012-09-12 Wed]
Changes in version 1.5.16
- parallel quantify is now always set to FALSE on Windows, fixing example checking issues [2012-09-11 Tue]
- fixed types in plotMzDelta man [2012-09-11 Tue]
Changes in version 1.5.13
- updated fillUp function [2012-08-15 Wed]
- added tikzDevice to suggests [2012-08-16 Thu]
- tikzDevice no longer on CRAN - removing from Suggests and using pdf as device in vignette [2012-08-16 Thu]
Changes in version 1.5.12
- using knitr instead of pgfSweave and misc vignette updated[2012-08-13 Mon]
- spectrum2 reporter plotting params updates [2012-08-14 Tue]
- added reporterNames to NAMESPACE [2012-08-14 Tue]
Changes in version 1.5.11
- type in filterNA log messaging and also rounding pNA [2012-06-07 Thu]
- typo in demo vignette - Gb instead of Mb [2012-07-15 Sun]
Changes in version 1.5.10
- Fixed readMSData instrumentInfo handling (reported by Gopuraja Dharmalingam) [2012-06-05 Tue]
- new multiple file loading test in test_io [2012-06-05 Tue]
Changes in version 1.5.9
- topN now properly updates processingData [2012-06-01 Fri]
- combineFeatures updates featureNames based on the groupBy argument - updated demo vignette and man accordinlgy [2012-06-01 Fri]
- additional parameters were not passed when normalise using vsn [2012-06-01 Fri]
Changes in version 1.5.8
- added aa data in environment data.frame [2012-05-22 Tue]
- fixed MSnbase:::subsetBy (used by topN) when ncol(object) == 1 [2012-05-25 Fri]
- new nQuants function [2012-05-31 Thu]
- minor vignettes updates [2012-05-31 Thu]
- nQuants now return a matrix with col names, taken form sampleNames(object) [2012-05-31 Thu]
Changes in version 1.5.7
- changed title method to exptitle to avoid conflict/confusion with graphics::title and consitency with expinfo method [2012-05-15 Tue]
- changed email to expemail [2012-05-15 Tue]
- Added rols to Suggests [2012-05-15 Tue]
Changes in version 1.5.6
- new ionSource, analyser, detectorType, title accessor methods for MIAPE, pSet and MSnSet classes [2012-05-06 Sun]
- updated quantify example to use data(itraqdata) instead of reading dummyiTRAQ.mzXML [2012-05-09 Wed]
- initial mzTab write support [2012-05-10 Thu]
- mzTab read support [2012-05-10 Thu]
- updated demo and io vignettes with mzTab info [2012-05-10 Thu]
Changes in version 1.5.5
- added email slot in MIAPE and accessor [2012-05-04 Fri]
- added expinfo methods to pSet and MSnSet [2012-05-04 Fri]
- updated itraqdata [2012-05-04 Fri]
- misc man typos fixed [2012-05-04 Fri]
- quantify now properly propagates processingData [2012-05-04 Fri]
Changes in version 1.5.4
- automatically populating experiment data instrument info while reading data [2012-04-30 Mon]
- msInfo fixed and exported [2012-04-30 Mon]
- update demo vignette with 14 fractions analysis paragraph [2012-05-01 Tue]
Changes in version 1.5.3
- extractSpectra is now defunct [2012-04-20 Fri]
- caching full header in level 1; this is required when and MSnExp instance with many spectra (created from many raw files) is quantified - calling header(object) is a too big overhead compared to actual reporter quantification. [2012-04-20 Fri]
- The header() method now uses the cached dataframe if level ]= 1; the (unexported) .header function can be used to generate the dataframe using the assayData slot data. [2012-04-20 Fri]
- Setting processingData in MSnSet initialisation. [2012-04-20 Fri]
- Dropping index column from header. [2012-04-20 Fri]
- new Spectrum class v0.2.0 has tic slot. [2012-04-21 Sat]
- tic method (data stored as a Spectrum slot) now returns total ion current (as commonly used) and total ion count is obtain using ionCount. [2012-04-21 Sat]
- fixed normalisation boxplot titles and other tic/ionCount changes in demo vignette. [2012-04-21 Sat]
- removed qual subetting in MSnSet’s “[” method [2012-04-24 Tue]
Changes in version 1.5.2
- transposing and MSnSet does silently drop the protocolData now [2012-04-03 Tue]
- fixed MSnExp pData creation for multiple files, feature names have a .fileNumber extension now. [2012-04-19 Thu]
- testing for uniqueness of files (filenames) in readMSData [2012-04-19 Thu]
- updated itraqdata.RData [2012-04-19 Thu]
- added a paralle argument to quantify and using paralle = FALSE in vignette, to avoid duplicated display of the command [2012-04-19 Thu]
- defined “reporterNames<-” generics [2012-04-19 Thu]
- fixed warning in readMSData where all not used for comparison of verctors of length ] 1 [2012-04-20 Fri]
Changes in version 1.5.1
- updated NA warning message in readIspyData [2012-03-05 Mon]
- fixed combineFeatures/combineMatrixFeatures for 1 sample [2012-03-20 Tue]
- image method for MSnSet instances [2012-03-20 Tue]
- fixed bug in plotNA (first t was wring) [2012-03-21 Wed]
- import plot from stats4 [2012-03-21 Wed]
- using reshape2 [2012-03-30 Fri]
MSnbase 1.3
Changes in version 1.3.15
- new updateFeatureNames function [2012-02-17 Fri]
- updated vignettes to illustrate vertical/horizontal combine [2012-02-17 Fri]
- typo in normalised.Rd [2012-02-19 Sun]
- TODO combine unit tests
Changes in version 1.3.14
- new is.na.MSnSet [2012-02-16 Thu]
- updated vignette and NA related man pages with cross-links [2012-02-16 Thu]
Changes in version 1.3.13
- new plotNA method + doc [2012-02-15 Wed]
- new filterNA method + doc + tests [2012-02-15 Wed]
- added a check on ‘n’ in topN [2012-02-16 Thu]
- created a .Rinstignore [2012-02-16 Thu]
- Update package Rd [2012-02-16 Thu]
Changes in version 1.3.11
- changed explicit close(file) in writeMgf methods to on.exit(close(file)) [2012-02-12 Sun]
- typo in vignette [2012-02-13 Mon]
Changes in version 1.3.10
- type in writeMgfData man [2012-02-07 Tue]
- updated TITLE in writeMgfData [2012-02-08 Wed]
Changes in version 1.3.9
- updated demo vignette [2012-02-03 Fri]
- sorting numeric subsets in “[” pSet, as unsorted numerical indexes fails [2012-02-03 Fri]
- Added match.arg in combineFeatures so that a unique default value (the first) is used when no fun is specified [2012-02-03 Fri]
Changes in version 1.3.8
- Modified trimMz warning to report acquisition number [2012-02-01 Wed]
- add ‘experimentData(object, value) <-’ method for signature eSet and MIAPE [2012-02-02 Thu]
- combine methods for MIAPE instances [2012-02-02 Thu]
- combine methods for MSnProcess instances [2012-02-02 Thu]
- changed qual drop warning into message in combineFeatures, updated test_MSnSet accordingly [2012-02-02 Thu]
- new updateFvarLabels and updateSampleNames function [2012-02-03 Fri]
- combine method for MSnSets [2012-02-03 Fri]
- Updated demo vignette figure 8 [2012-02-03 Fri]
Changes in version 1.3.7
- Speeded up writeMgfData [2012-01-28 Sat]
- fixes for ggplot2 0.9.0
- added import(grid) and import(reshape) [2012-01-30 Mon]
- importFrom(plyr, …) instead of only llply [2012-01-31 Tue]
- loading reshape and grid in vignette [2012-01-31 Tue]
- fixed chunk 21 (label = quantitation-plot) [2012-01-31 Tue]
Changes in version 1.3.6
- Updated NoteAboutSpeedAndMemory since parallel processing has been added. [2011-12-18 Sun]
- Added CITATION [2012-01-27 Fri]
- Added information to header output: acquisition number and precursor intensity [2012-01-27 Fri]
- Added a test in plot.Spectrum2 for empty dataframe [2012-01-27 Fri]
- moved foreach, doMC to enhances [2012-01-27 Fri]
Changes in version 1.3.5
- added a gc() before mzR::close(msdata)… seems to help with Rcpp and ref classes issue. [2011-12-09 Fri]
- added a show parameter to getCacheEnv to define .cache should be printed out before being returned. [2011-12-09 Fri]
- added cache unit test [2011-12-09 Fri]
- readMzXMLData is now defunct and remove xcms from Imports [2011-12-16 Fri]
Changes in version 1.3.4
- fixed bug in show MSnExp method for MS1 experiments. When loading MS1 spectra, cache is set to 0. Bug reported by Jesse Meyer. [2011-12-06 Tue]
- fixed another bug/typo in readMSData [2011-12-06 Tue]
- now running extractSprectum example again [2011-12-06 Tue]
- setting default cache to 0, as cache=1 introduces unstabel behavious… will investigate that [2011-12-06 Tue]
Changes in version 1.3.3
- added parallel computation for MSnExp quantitation using foreach with llply(…, .parallel=TRUE) [2011-12-03 Sat]
- TODO document above in quantify-methods.Rd
- added foreach and doMC in Suggests [2011-12-03 Sat]
- added Spectrum removePeaks and clean’ing in readMSData [2011-12-05 Mon]
Changes in version 1.3.2
- extractSpectrum example, as this seems to be a major offender producing the intermittent check ‘Error in function (x) : attempt to apply non-function’ error [2011-11-07 Mon]
- typo in Author@R [2011-11-14 Mon]
- modified utils.removePeaks and utils.clean to call sapply instead of IRanges:sapply [2011-12-01 Thu]
MSnbase 1.1
Changes in version 1.1.27
- fixed bug in readIspyData [2011-10-07 Fri]
- removed (unexported) ratio code [2011-10-12 Wed]
- added processing description when MSnSet[’ing [2011-10-12 Wed]
- man typos corrected [2011-10-14 Fri]
- changed readMzXMLData to readMSData in tests [2011-10-14 Fri]
- expecting warning for readMzXMLData in test_io [2011-10-14 Fri]
Changes in version 1.1.26
- extractSpectra deprecated [2011-10-05 Wed]
- small changes in cache.R functions [2011-10-05 Wed]
- changed [, extractSpectra and extractPrecSpectra to update the .cache slot [2011-10-05 Wed]
- MSnExp show method uses .cache when level==1. [2011-10-05 Wed]
- Finished level 1 cache implementation: leads to an average 11.8 times faster MSnExp show method. [2011-10-05 Wed]
Changes in version 1.1.25
- added .cache slot to pSet class [2011-10-03 Mon]
- added pSet initialize method to set .cache and .cache$level as ‘0’. [2011-10-03 Mon]
- Check that level is defined in .cache and env is locked in pSet validity method. [2011-10-03 Mon]
- updated itraqdata.RData [2011-10-03 Mon]
- Deprecated readMzXMLData, added defunct.Rd [2011-10-03 Mon]
- changed readMzXMLData to readMSData in man [2011-10-03 Mon]
- updated show MSnExp for speed [2011-10-03 Mon]
- updated read*Data is support cache = [0|1]. [2011-10-03 Mon]
- updated precScanNum to use sapply(spectra(…), precScanNum) instead of unlist(eapply(assayData(…), precScanNum)) to preserve splectra order. [2011-10-03 Mon]
- new cache.R file with @.cache related code [2011-10-03 Mon]
Changes in version 1.1.24
- in readMgfData, SCANS is not used to populate acquisitionNum anymore, as several scans might have been combined upstreams [2011-09-26 Mon]
- added fillUp function in utils.R and exported [2011-09-27 Tue]
- new MSnbase-io vignette [2011-09-28 Wed]
Changes in version 1.1.23
- fixed writeMgfData(“MSnExp”) [2011-09-21 Wed]
- readMgfData now works when mz and intensty are separated by a ’ (as exported by PRIDE Inspector) [2011-09-21 Wed]
- show(“MSnExp”) now works without retention time [2011-09-21 Wed]
- updated mgf2Spectrum2 to make it faster [2011-09-21 Wed]
- fixed missing fromFile slot in data created from readMgfData that prevented calling header [2011-09-21 Wed]
- readMgfData now creates a fData based on the peak header [2011-09-21 Wed]
- modified getCurveWidth to work with centroided data [2011-09-21 Wed]
- fixed bug getCurveWidth [2011-09-21 Wed]
Changes in version 1.1.22
- removed (internal) Mascot query link column in readIspyData to work with latest ouput version [2011-09-12 Mon]
- removed the fillUp part in readIspyData [2011-09-14 Wed]
- exported readIspyData [2011-09-20 Tue]
- removed link to proteomics sig list [2011-09-20 Tue]
- removed url in DESCRIPTION [2011-09-20 Tue]
- Spectrum2 slot ms1scan renamed to precScanNum and populated using mzR::header()$precursorScanNum. Updated affected methods/functions and manual pages. New accessor method precScanNum is exported. THIS CHANGE IS NOT COMPATIBLE WITH PREVIOUSLY CREATED MSnSet -BJECTS! [2011-09-20 Tue]
Changes in version 1.1.21
- updated write.exprs to add fData columns [2011-09-08 Thu]
- added write.exprs and readMSnSet unit test [2011-09-08 Thu]
Changes in version 1.1.20
added a readMSnSet function [2011-09-08 Thu]
added a write.MSnSet(“MSnSet”) method [2011-09-08 Thu]
vignette/man updates - mainly data import section documenting readMSData and readMgfData [2011-09-08 Thu]
incorporating mzR io frame work [2011-09-05 Mon]
use mzR’s peaksCount and header generics [2011-09-05 Mon]
added test to check that readMzXMLData and readMSData give same output [2011-09-05 Mon]
added readMSData.Rd doc file [2011-09-05 Mon]
added Author@R field in DESCRIPTION [2011-09-07 Wed]
compressed/resaved (using resaveRdaFiles) itraqdata.RData file to [2011-09-07 Wed]
Changes in version 1.1.18
- read support for mgf files contributed by Guangchuang Yu [2011-07-06 Wed]
- added as.ExpressionSet.MSnSet and setAs methods and updated MSnSet doc [2011-07-09 Sat]
- fixed read/write mgf compatibility [2011-09-01 Thu]
- added mgf io test [2011-09-01 Thu]
- exported and document mfg read/write support [2011-09-01 Thu]
- added centroided parameter to rawToSpectrum[1|2] to set this directly at object creation in readMzXmlData [2011-09-01 Thu]
- other minor changes in Rd files [2011-09-01 Thu]
- added warning checks for combineFeatures when verbose=TRUE in test_MSnSet.R [2011-09-02 Fri]
Changes in version 1.1.17
- updated itraqdata manual [2011-06-27 Mon]
- fixed bug in MSnSet validity method - msg was initialised to NULL when testing Biobase:::isValidVersion and Biobase::assayDataValidMembers [2011-07-02 Sat]
- added t.MSnSet method [2011-07-02 Sat]
- document t.MSnSet method [2011-07-05 Tue]
- test for t-MSnSet [2011-07-05 Tue]
- new “[”-MSnSet method to properly subset qual slot [2011-07-06 Wed]
- updated MSnSet validity method to check qual dims [2011-07-06 Wed]
- combineFeatures now drops the spectrum-specific qual slot [2011-07-06 Wed]
- test for “[”-MSnSet [2011-07-06 Wed]
Changes in version 1.1.16
- added addVigs2WinMenu call in .onAttach [2011-06-26 Sun]
- added plotMzDelta paragraph in vignette [2011-06-26 Sun]
Changes in version 1.1.15
- new names and description methods for ReporterIons [2011-06-16 Thu]
- added validObject() checks [2011-06-16 Thu]
- new removeReporters method [2011-06-16 Thu]
- plotMzDelta is exported and documented [2011-06-17 Fri]
Changes in version 1.1.14
- Adding plotMzDelta QC plot (not yet exported), contributed by Guangchuang Yu [2011-06-14 Tue]
- created a locked environment to store amino.acids dataframe [2011-06-14 Tue]
- TODO plotMzDelta documentation and vignette section - man DONE in v 1.1.15 , vignette DONE in v 1.1.16
Changes in version 1.1.13
- changed pSet [[ method [2011-06-13 Mon]
- additional updates pSet [[ method [2011-06-13 Mon]
- added MSnExp subsetting error tests [2011-06-13 Mon]
- created new plotting-dataframe.R file with former plotting utils functions, now renamed plot*.header [2011-06-13 Mon]
Changes in version 1.1.12
- added invisible(NULL) to all show methods [2011-06-08 Wed]
- added centroided argument to plot.MSnExp [2011-06-09 Thu]
Changes in version 1.1.11
- harmonised MSnExp and Spectrum plot axes labels [2011-05-18 Wed]
- Added plotting customisation section in vignette [2011-05-18 Wed]
- updated signature of plot2d method to “MSnExp” only [2011-05-18 Wed]
- added/exported plotDensity methods [2011-05-18 Wed]
- started QC vignette section [2011-05-18 Wed]
- added preprocSelection and preprocSelectionTable functions [2011-05-18 Wed]
- TODO document preprocSelection[Table] in vignette
- reduces plot2d-figure and plotDensity-figure sizes using png [2011-05-19 Thu]
- added plotDensity doc [2011-05-19 Thu]
- added round param to preprocSelection[Table] [2011-05-19 Thu]
- preprocSelection[Table] documented and exported [2011-05-19 Thu]
- fixed bug in plot.Spectrum1 [2011-05-24 Tue]
- changed removePeaks setGeneric explicit signature [2011-05-26 Thu]
- added MassSpectrometry biocView [2011-05-27 Fri]
Changes in version 1.1.10
- minor updates in demo vignette [2011-05-13 Fri]
- added plot argument to plot methods [2011-05-16 Mon]
- fix in makeImpuritiesMatrix [2011-05-16 Mon]
- added meanSdPlot MSnSet method [2011-05-17 Tue]
- minor cosmetic fix in purityCorrect error message [2011-05-17 Tue]
- added method=“sum” to Spectrum/MSnExp normalisation [2011-05-17 Tue]
- typo in MSnSet-class.Rd corrected [2011-05-17 Tue]
Changes in version 1.1.9
- exporting normali[s|z]e methods for MSnSet, Spectrum and MSnExp [2011-05-12 Thu]
- added quantile normalisation [2011-05-12 Thu]
- added quantile.robust normalisation [2011-05-12 Thu]
- added vsn2 normalisation [2011-05-12 Thu]
- added normalise manual [2011-05-12 Thu]
- included normalisation section in vignette [2011-05-13 Fri]
- more vignette updates [2011-05-13 Fri]
- updated plotting methods to round MZ in title [2011-05-13 Fri]
Changes in version 1.1.8
- added writeMgfData method from spectra and experiment [2011-05-09 Mon]
- added writeMgfData manual [2011-05-09 Mon]
- added itraqdata data set and updated vignette to use it [2011-05-11 Wed]
- updated man pages to use tiny dummyiTRAQ.mzXML [2011-05-11 Wed]
- added makeImpuritiesMatrix function [2011-05-11 Wed]
Changes in version 1.1.7
- reporter ions purity correction method, man and test [2011-05-09 Mon]
- updated vignette [2011-05-09 Mon]
Changes in version 1.1.6
- added incomplete dissociation and spectral counting sections to demo vignette [2011-05-06 Fri]
- added bioc-sig-proteomics link to foreword [2011-05-06 Fri]
- type in foreword [2011-05-06 Fri]
Changes in version 1.1.4
- readIspyData updated to return updated factors [2011-05-03 Tue]
- added unexported/undocumented combineFeatures function for MSnSets [2011-05-03 Tue]
- added basic tests for combineFeatures [2011-05-03 Tue]
- added combineFeatures manual [2011-05-04 Wed]
- exportig combineFeatures [2011-05-04 Wed]
Changes in version 1.1.3
- as.data.frame.Spectrum columns now are (first) mz and (second) intensity [2011-04-27 Wed]
- exporting as.data.frame.Spectrum and coerce [2011-04-27 Wed]
Changes in version 1.1.2
- Simplified quantify generic signature - now only object argument [2011-04-19 Tue]
- Added strict parameter to quantify method, man updated, added relevant test
- Added illustrative plot for quantitation methods in MSnbase-demo vignette [2011-04-19 Tue]
- Added illustrative plot for data pre-processing (removePeaks and clean) in MSnbase-demo vignette [2011-04-20 Wed]
- No warnings are issued anymore when peaks expands outside of mz(reporters) +/- width(reporters). See ?quantify on how to check this manually. [2011-04-19 Tue]
- No warnings are issued anymore when reporter peaks are missing. See ?quantify on how to check this manually. [2011-04-20 Wed]
- pSet validity warns if length(unique(msLevel(object))) ] 1, rather than != 1. The latter triggered a warning for a new(“MSnExp”). [2011-04-20 Wed]
Changes in version 1.1.1
- added setAs data.frame and as.data.frame methods for Spectrum objects [2011-03-29 Tue]
- support for uncentroided MS2 spectra plots [2011-03-31 Thu] [2011-04-02 Sat]
- support for uncentroided MS1 spectra plots [2011-04-02 Sat]
- minor modification to readIspyData [2011-04-04 Mon]
- removed centroided slot from MSnProcess and added to individial Spectrum instances. Relevant for Velos HCD (profile)/CID (uncentroided) data [2011-04-04 Mon]
- modified readMzXmlData accordingly [2011-04-04 Mon]
- added validObject(new(…)) tests for each class [2011-04-04 Mon]
- added centroided[<-] methods to Spectrum and pSet [2011-04-04 Mon]
- added ‘keepAll’ parameter to readIspyData [2011-04-11 Mon]
MSnbase 0.99
Changes in version 0.99.2
- updated references in package Rd [2011-03-24 Thu]
- added readIspyData.Rd [2011-03-24 Thu]
- removed old readMzXMLData function [2011-03-24 Thu]
- cleaning up code [2011-03-24 Thu]
- fixed MSnSet initialize: setting experimentData as MIAPE [2011-03-25 Fri]
- fixed MSnSet initialize: identical featureNames in assayData and featureData for empty MSnExp istances [2011-03-25 Fri]
- better test organisation and added object validity tests [2011-03-25 Fri]
- updated readIspyData function [2011-03-25 Fri]
Changes in version 0.99.1
- fake vignettes are copied back in inst/doc/. to make sur tar tarball can be extracted and build again [2011-03-24 Thu]
- Making clean after make all [2011-03-24 Thu]
Changes in version 0.99.0
- MSnProcess@process get’s one line when subsetting and MSnExp object [2011-03-21 Mon]
- Updated vignette Makefile [2011-03-22 Tue]
- Added fake vignettes [2011-03-22 Tue]
- Version set to 0.99.0 [2011-03-22 Tue]
- Minor changes in quantify-method.Rd [2011-03-22 Tue]
- added .Rbuildignore to ignore ’sweave-cache.*’ [2011-03-22 Tue]
- added R/zzz.R with start-up message [2011-03-23 Wed]
- Added width generic [2011-03-23 Wed]
- IRanges in now imported [2011-03-23 Wed]
MSnbase 0.1
Changes in version 0.1.5
- added zoo to Suggest, as zoo::rollapply is used in vignette.
- changes rollapply call to zoo:::rollapply.zoo, to make it work with zoo_1.6-4, rather that depending on zoo_1.7-0, which is not yet on CRAN (only r-forge).
- added vns to Suggests, as it is used in the demo vignette.
Changes in version 0.1.3
- Updates to ReporterIons man page
- Moved some Depends to Imports and updated NAMESPACE
- corrected a IRanges:::sapply ot IRanges::sapply in utils.R
- added inst/tests/test_MSnProcess.R
Changes in version 0.1.2
- MSnProcess@MSnbaseVersion is not set in the initialize method instead to the prototype
- changed R CMD to $(R_HOME)/bin/R CMD in inst/doc/Makefile
- removed first and last (was 5th) MS1 spectra and associated MS2 spectra from dummy file to reduce size below 2MB.
- Updated tests to reflect new dummy data set
- Edition of dummy brakes readMzXMLData with msLevel=1 – comment related tests
- Updated MSnbase-demo vignette and man to use good spectra un plots (i.e “X43” instead of “X64”)