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# MSnbase 2.9
Changes in version 2.9.3
- Fix bug in ms2df (order of fcols could be scambled) <2018-12-04 Tue>
- Fix bug in MSnSet constructor (see issue #386) <2018-12-07 Fri>
- Add filterPolarity method (see issue #388, feature requeste by
@zeehio) <2018-12-10 Mon>
Changes in version 2.9.2
- Fix problem that impute(x, method="knn") sets the seed (issue
#380). Contributed by
Constantin Ahlmann-Eltze
<2018-11-16 Fri>
- Conserve spectra names in `combineSpectra` (see
#379) <2018-11-15 Thu>
- Fix bug in writeMSData - see #383 <2018-11-22 Thu>
Changes in version 2.9.1
- Add clean,Chromatograms (issue
#354) <2018-11-07 Wed>
- Add as,Spectra,list as,Spectra,MSnExp and as,MSnExp,Spectra
(issue #370) <2018-11-07 Wed>
- Add filterMsLevel,Spectra <2018-11-07 Wed>
- Fix regression bug in plot,Spectrum1 <2018-11-14 Wed>
Changes in version 2.9.0
- New version for Bioc 3.9 devel
# MSnbase 2.8
Changes in version 2.8.0
- New version for Bioc 3.8 release
# MSnbase 2.7
Changes in version 2.7.12
- Fix warnings on windows (see
#371) <2018-10-26 Fri>
- Add parameter ppm to consensusSpectrum and meanMzInts (see
#373 for details)
<2018-10-26 Fri>
Changes in version 2.7.11
- Change default for `timeDomain` in `combineSpectra` and
`combineSpectraMovingWindow` to `FALSE` <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 2.7.10
- Methods for Spectra class <2018-10-15 Mon>
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 2.7.8
- MGF exporter gets a new `addFields` argument (see PR
#362) <2018-10-12 Fri>
- New `Spectra` (`SimpleList` of `Sepctrum` objects) (see PR
#361) <2018-10-13 Sat>
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>
Changes in version 2.7.2
- Handle files without any spectra - see
#342
<2018-05-15 Tue>
- New `mergeFeatureVars` and `expandFeatureVars` functions
<2018-05-30 Wed>
- Update plot,Spectrum methods to match the tolerance and relative
arguments (see #350) <2018-06-29 Fri>
Changes in version 2.7.1
- Version bump to force new vignette build
Changes in version 2.7.0
- New devel version for Bioc 3.8
# MSnbase 2.6
Changes in version 2.6.0
- New release version for Bioc 3.7
# MSnbase 2.5
Changes in version 2.5.15
- Nothing yet.
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 `combineFeatures` contributed by
Ludger Goeminne, Adriaan Sticker and Lieven Clement <2018-04-03 Tue>
- Adapt `utils.removePeaks` to new `IRanges` implementation; 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 `timeDomain` to `combineSpectra`, `combineSpectraMovingWindow`
and `estimateMzScattering` allowing 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 for `pSet` (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 `featureData` slot, accessible with
`fData` to store metadata for the individial MSnSets of the
list. `MSnSetList` also not has an `sapply` method. <2018-01-10 Wed>
- combineFeatures now has a new `fcol` argument (see issue #195)
<2018-01-11 Thu>
Changes in version 2.5.3
- Add filterPrecursorScan for `MSnExp` and `OnDiskMSnExp`;
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_max` to 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
Changes in version 2.5.0
- New version for Bioc 3.7 (devel)
# MSnbase 2.4
Changes in version 2.4.0
- New version for Bioc 3.6 (release)
# MSnbase 2.3
Changes in version 2.3.14
- Use `normalizePath` to force absolute file paths in `readMSData`.
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 `protocolData` in isobaric quantification; fixes #265
Changes in version 2.3.11
- Amend `addIdentificationData` when sourceInfo reports multiple files
and when scores are missing from the identification results (closes
#261).
- Don't overwrite `processingData` slot when creating an `MSnSet` object
(closes #264).
Changes in version 2.3.10
- New `isCentroidedFromFile` function <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>
- `calculateFragments` now just calculate fragments for all `n - 1L` bonds
(before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun>
- Add `isEmpty` methods for `Chromatogram` and `Chromatograms` objects
<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 2.3.8
- New infrastructure for chromatogram data <2017-06-24 Sat>
- Change naming scheme for spectra: FFILEID.SSPECTRUMID, e.g. F01.S0001. Before
it has been XSPECTRUMID.FILEID. The new naming scheme changes the order of
the spectra. See #255 (and PR #256) for details <2017-06-25 Sun>.
Changes in version 2.3.7
- export filterEmptySpectra
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 2.3.5
- Fix superscript syntax in demo vignette <2017-06-14 Wed>
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 `getColsFromPattern` and `getRowsFromPattern` and add unit tests
<2017-05-11 Thu>.
- Add `.filterNA` and rewrite `filterNA` for `matrix` and `MSnSet`
<2017-05-11 Thu>.
- Convert main MSnbase-demo vignette to Rmd/html <2017-05-27 Sat>
- `naplot` gains a `reorderRows` and `reorderColumns` argument
<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>.
Changes in version 2.3.1
- Introduce "NTR" method for `combineFeatures` <2017-04-26 Wed>.
- Rewrite `nQuants` and `featureCV` to avoid returning of rows for empty
factors; see PR #208 for details <2017-04-28 Fri>.
- Add $,pSet method to easily access columns in the phenoData (see #203)
Changes in version 2.3.0
- Version bump for new Bioc devel.
# MSnbase 2.2
Changes in version 2.2.0
- Version bump for Bioc release version 3.5.
# 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 2.1.18
- suggest reshape2, as it's used in vignette <2017-04-18 Tue>
Changes in version 2.1.17
- Update NEWS file <2017-04-11 Tue>
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, `getTopIdx` and `subsetById` are 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 2.1.13
- Internal rewrite and speedup of plotNA <2017-02-26 Sun>
Changes in version 2.1.12
- Import dist from stats <2017-02-25 Sat>
- Fix filing example <2017-02-25 Sat>
Changes in version 2.1.11
- Fix breaks calculation for binning single (closes #191) and multiple
(closes #190) spectra. The fix for single spectra (#191) could result in
slightly different breaks on the upper end of the m/z values. <2017-02-10 Fri>
- New `aggvar` function, to assess aggregation variability
<2017-02-11 Sat>
Changes in version 2.1.10
- New `diff.median` normalisation for `MSnSet`s. <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 2.1.5
- Fix (unexported) navMS example code <2016-12-14 Wed>
Changes in version 2.1.4
- Jo added netCDF support <2016-11-30 Wed>
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>
Changes in version 2.1.1
- Fix typo in impute man page <2016-10-19 Wed>
- Cite Lazar 2016 in vignette imputation section <2016-10-28 Fri>
Changes in version 2.1.0
- New version for Bioconductor devel
# MSnbase 2.0.0
- New version for Bioconductor release version 3.4
# MSnbase 1.99
Changes in version 1.99.6
- Reverting to old initialize,Spectrum (see issue #163)
<2016-10-07 Fri>
- Setting Spectrum class versions outside of prototype (see issue
#163). For this, there is now a vector of class version in
.MSnbaseEnv <2016-10-10 Mon>
Changes in version 1.99.5
- Add removeReporters,OnDiskMSnExp (see issue #161 for details)
<2016-10-07 Fri>
Changes in version 1.99.4
- Fix bug in readMzTabData_v0.9 <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`, `pch` for 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 1.21.2
- Check for rownames/fnames in readMSnSet2 and unit test
<2016-05-05 Thu>
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>
Changes in version 1.21.0
- Version bump for new Bioc devel
# MSnbase 1.20
Changes in version 1.20.0
- Version bump for Bioc release version 3.3
# MSnbase 1.19
Changes in version 1.19.24
- more unit tests and bug fixes <2016-04-30 Sat> <2016-05-02 Mon>
Changes in version 1.19.23
- more unit tests and bug fixes <2016-04-27 Wed> <2016-04-28 Thu>
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 1.19.21
- nadata.R unit tests and bugs fixed <2016-04-22 Fri>
Changes in version 1.19.20
- Moved makeNaData[2] and whichNA (was in pRoloc) <2016-04-21 Thu>
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 1.19.18
- fix typo in man <2016-04-02 Sat>
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 1.19.14
- Document change in nQuants param fcol to groupBy <2016-03-02 Wed>
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 1.19.10
- export exprs, fvarLabels, and sampleNames[<-] <2016-01-30 Sat>
Changes in version 1.19.9
- new trimws method for data.frames and MSnSets <2016-01-29 Fri>
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 1.19.4
- Replacement method for MSnSetList names <2015-11-24 Tue>
Changes in version 1.19.3
- New argument fcol to selectFeatureData to select feature variables
using a vector <2015-10-28 Wed>
Changes in version 1.19.2
- new selectFeatureData function to subset the feature data
<2015-10-24 Sat>
Changes in version 1.19.1
- Remove generics that are defined in ProtGenerics <2015-10-15 Thu>
Changes in version 1.19.0
- Bioc devel 3.3
# MSnbase 1.18
Changes in version 1.18.0
- Bioc release 3.2
# 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 1.17.15
- Fix typo in plot man <2015-08-23 Sun>
Changes in version 1.17.14
- Fix typo in impute man <2015-08-17 Mon>
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 1.17.12
- fix show MIAPE when some otherInfo at NA <2015-07-15 Wed>
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 1.17.10
- Fix URL <2015-06-30 Tue>
Changes in version 1.17.9
- calculateFragments' "neutralLoss" argument is now a list (was a logical
before), see #47. <2015-06-24 Wed>
- add defaultNeutralLoss() function to fill calculateFragments' modified
"neutralLoss" argument, see #47. <2015-06-24 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 1.17.7
- Fix support of identification-only mzTab files <2015-06-22 Mon>
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>
Changes in version 1.17.3
- iTRAQ 8-plex correction factors and impurity matrix
<2015-05-22 Fri>
Changes in version 1.17.2
- new filterZero function <2015-05-01 Fri>
Changes in version 1.17.1
- new MSnSetList class <2015-04-19 Sun>
- new commonFeatureNames function <2015-04-14 Tue>
- new compareMSnSets function <2015-04-19 Sun>
- splitting and unsplitting MSnSets/MSnSetLists <2015-04-19 Sun>
Changes in version 1.17.0
- new devel version for Bioc 3.2
# 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 1.15.17
- add TMT10 paragraph and fig to demo vignette [2015-04-09 Thu]
Changes in version 1.15.16
- support for TMT10 plex [2015-04-08 Wed]
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 1.15.11
- update malformed Description [2015-03-20 Fri]
Changes in version 1.15.10
- update compareSpectra man [2015-03-19 Thu]
- ExpressionSet <-> MSnSet coercion [2015-03-19 Thu]
Changes in version 1.15.9
- use S4Vectors' isEmpty generic [2015-03-10 Tue]
Changes in version 1.15.8
- Improved imputation section in demo vignette [2015-03-05 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]
Changes in version 1.15.0
- Devel version for Bioc 3.1
# MSnbase 1.14
Changes in version 1.14.0
- Release version for Bioc 3.0
# 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 1.13.13
- fix issue with readMSnSet2 without fdata [2014-07-28 Mon]
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 1.13.11
- remove Vennerable::Venn from example and DESCRIPTION [2014-06-19 Thu]
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 1.13.8
- Add recommended biocView [2014-06-05 Thu]
Changes in version 1.13.7
- Bug tracking link [2014-05-26 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]