Changes in version 2.10.1
-------------------------
- Fix bug in `calculateFragments` for neutral loss calculation. For the
"loss of water" the mass of HO~2~ instead of H~2~O was removed (see #462).
Thanks to Max Helf (@mjhelf) for the fix (see #463) <2019-05-31 Fri>.
Changes in version 2.9.6
------------------------
- remove plain NEWS file now that R supports NEWS.md
Changes in version 2.9.5
------------------------
- Add `isolationWindowLowerMz` and `isolationWindowUpperMz` methods <2019-04-15 Mon>
- Add `filterPrecursorMz` method <2019-04-15 Mon>
- Add `filterIsolationWindow` method <2019-05-16 Tue>
Changes in version 2.9.4
------------------------
- Remove `NAnnotatedDataframe` <2019-04-10 Wed>
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
Changes in version 2.8.0
------------------------
- New version for Bioc 3.8 release
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
Changes in version 2.6.0
------------------------
- New release version for Bioc 3.7
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)
Changes in version 2.4.0
------------------------
- New version for Bioc 3.6 (release)
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.
Changes in version 2.2.0
------------------------
- Version bump for Bioc release version 3.5.
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
- New version for Bioconductor release version 3.4
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>
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
Changes in version 1.20.0
-------------------------
- Version bump for Bioc release version 3.3
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
Changes in version 1.18.0
-------------------------
- Bioc release 3.2
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
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
Changes in version 1.14.0
-------------------------
- Release version for Bioc 3.0
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]
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 1.13.3
-------------------------
- FeaturesOfInterest [2014-04-29 Tue]
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]
Changes in version 1.13.1
-------------------------
- add precursor method to Spectrum2 normalisation method [2014-04-08 Tue]
- add smooth for MSnExp and Spectrum classes [2014-04-10 Thu]
- add pickPeaks for MSnExp and Spectrum classes [2014-04-10 Thu]
- updated show,MSnExp to display only first/last files when > 2 [2014-04-11 Fri]
Changes in version 1.13.0
-------------------------
- New devel version for Bioc 3.0
Changes in version 1.11.14
--------------------------
- update dependency to R >= 3.1 [2014-04-05 Sat]
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 1.11.7
-------------------------
- NA
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]
Changes in version 1.11.3
-------------------------
- updated mzTab example files to new url [2013-11-15 Fri]
- warning about mzTab versions [2013-11-15 Fri]
Changes in version 1.11.2
-------------------------
- move inst/doc to vignettes [2013-10-19 Sat]
Changes in version 1.11.1
-------------------------
- document na.rm in combineFeatures Rd [2013-10-18 Fri]
Changes in version 1.11.0
-------------------------
- New devel version for Bioc 2.14
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 1.9.5
------------------------
- typo in Author[s]@R [2013-05-15 Wed]
Changes in version 1.9.4
------------------------
- new simple MSnSet constructor [2013-05-07 Tue]
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]
Changes in version 1.9.1
------------------------
- new logging utility function to update an MSnSet's
processingData(object)$processing [2013-03-29 Fri]
- Proper logging in t.MSnSet [2013-03-29 Fri]
Changes in version 1.9.0
------------------------
- new Bioc 2.13 devel version
Changes in version 1.8.0
------------------------
- new Bioc 2.12 stable version
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 1.7.22
-------------------------
- msnbase.r na.rm arg [2013-02-20 Wed]
Changes in version 1.7.21
-------------------------
- Added impute method [2013-02-19 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 1.7.16
-------------------------
- fixing knitr 1.0 compatibility [2013-01-15 Tue]
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 1.7.6
------------------------
- Fixed bug in readIspyData, reported by
Claire Mulvey [2012-11-27 Tue]
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]
Changes in version 1.7.3
------------------------
- updating readMzTabData to properly capture
experiment description [2012-10-12 Fri]
Changes in version 1.7.2
------------------------
- fixed readMSData for MS1 [2012-10-08 Mon]
Changes in version 1.7.1
------------------------
- fixed vignettes [2012-10-02 Tue]
Changes in version 1.7.0
------------------------
- Version bump for next devel release [2012-10-01 Mon]
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 1.5.15
-------------------------
- updating code to ggplot2 v0.9.2 [2012-09-07 Fri]
Changes in version 1.5.14
-------------------------
- added platform test to use doMC (d.tenenbaum) [2012-08-31 Fri]
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]
Changes in version 1.5.0
------------------------
- new devel version bump
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 1.3.12
-------------------------
- new topN methods + doc + tests [2012-02-14 Tue]
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
------------------------
- \dontrun{} 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]
Changes in version 1.3.1
------------------------
- Herve added BioGenerics as a dependency and import
statement in NAMESPACE [2011-11-29 Tue]
Changes in version 1.3.0
------------------------
- Version bump for Bioc 2.10 devel
Changes in version 1.2.0
------------------------
- Version bump for Bioc 2.9 release
Changes in version 1.1.28
-------------------------
- added pgfSweave to Suggests [2011-10-23 Sun]
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 '\t' (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 1.1.5
------------------------
- added combineFeatures example in demo vignette [2011-05-05 Thu]
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]
Changes in version 0.99.4
-------------------------
- removed pgfSweave from Suggests field [2011-04-04 Mon]
Changes in version 0.99.3
-------------------------
- Using Sweave rather than pgfSweave to build on lamb1. [2011-03-28 Mon]
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]
Changes in version 0.2.0 [2011-03-17 Thu]
-----------------------------------------
- MSnSet now extends eSet, reimplementing the ExpressionSet class
with exception of the experimentData slot, that must now be a MIAPE
instance.
- updated MIAPE substantially and added accessor methods.
- updated docs and vignettes to reflect above changes.
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 0.1.4
------------------------
- added pgfSweave to Suggests, as is called in vignette Makefile
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")
Changes in version 0.1.1
------------------------
- Added LazyLoad: yes in DESCRIPTION and modified docs accordingly
- Added NEWS file
Changes in version 0.1.0
------------------------
- Added MSnbase-demo vignette
- Added MSnbase-development vignette