NEWS.md
In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase 2.33

Fix the pheplus1 code chunk in MSnbase-demo vignette to handle the new Rdispo::getIsotope() list return value.

Add functionality to convert a Spectra object to a MSpectra.
Suggest pRolocdata (>= 1.43.2.1) (that has some extdata, needed to other packages' vignettes).

New Bioc devel version

MSnbase 2.31

Disable nested parallel processing for chromatogram() method.
Fix Rd notes.

New Bioconductor devel.

MSnbase 2.29

Move XML to suggests.

Remove parts of XML dependency.

Use fragmentation functions from PSMatch.
Mention R for Mass Spectrometry in start-up message.

Check for identical ion header in readMgfData() (see issue 597).

New devel

MSnbase 2.27

Fix declarations of centroided/smoothed setters for OnDiskMSnExp objects (from Hervé Pagès via Github).

New devel

MSnbase 2.25

Fix bug in descendPeaks (see #583)

Fix remote mztab filename.

New devel (Bioc 3.17)

MSnbase 2.24

New release (Bioc 3.16)

MSnbase 2.23

Fix robust aggregation for MsCoreUtils 1.9.2.

Import spectrapply generic from ProtGenerics.

New release (Bioc 3.16)

MSnbase 2.22

New release (Bioc 3.15)

MSnbase 2.21

Fix mz calculation in calculateFragments for neutral losses with a charge > 1 (see issue 573).

Allow different orientation of axis labels in image2 (see issue 571).

Adapt to changes in mzR version 2.29.3.

Add transformIntensity function for Chromatogram and MChromatograms objects.

Fix bug (issue #561).

Fix bug in compareChromatograms that creates a non-symmetric similarity matrix.

Change default for MSnbase fast load variable: set to TRUE also on macOS.

MSnbase 2.19

Fix plot with type = "XIC" to create an empty plot for samples without data points (issue #549).

Add compareChromatograms method.

MSnbase 2.17

Nothing yet

Bump to force propagation on Bioc

Import ProcessingStep from ProtGenerics.

Import quantify generic from ProtGenerics.
Fix defaults in calculateFragments man page (see issue #537).

Re-implement impute,MSnSet-method with MsCoreUtils::impute_matrix().
Re-implement normalise,MSnSet-method with MsCoreUtils::normalize_matrix().
Illustrate ReporterIons class using TMT16.
Re-implement formatRt() using MsCoreUtils::formatRt().
Use MsCoreUtils::robustSummary() (deleted code in this package).
Use MsCoreUtils::medianPolish().

Add normalize,Chromatogram method.
Add filterIntensity,Chromatogram method.
Add align,Chromatogram method.
Use two digits when printing retention time seconds

Add TMT16 reporter ions (contribute by Miguel Cosenza-Contreras)

Use ProtGenerics::calculateFragments generic
Document differences between spectrumId (spectrumID), acquitisionNum and scanIndex.

New Bioc devel version

MSnbase 2.15

Fixed some consistency in the processing reporting (contributed by @stanstrup).

Add extractSpectraData function to extract all data from an MSnExp or Spectra object as a DataFrame to be used with the Spectra package.

combineSpectraMovingWindow gains parameter ppm to allow definition of m/z relative differences.

Add splitByFile,OnDiskMSnExp method to provide a more efficient splitting.

Rename Spectra class to MSpectra.
Rename Chromatograms class to MChromatograms.

Add MSnbase2 citation entry <2020-05-15 Fri>

Fix: don't read mzTab twice <2020-05-05 Tue>

Bioconductor devel version (Bioc 3.12)

MSnbase 2.14

Bioconductor release version (Bioc 3.11)

MSnbase 2.13

Typo in OnDiskMSnExp man page <2020-04-26 Sun>
Fix plot,[On]MSnExp for centroided data <2020-04-26 Sun>
Use free x scaling in plot,MSnExp's facet <2020-04-26 Sun>

Remove duplicated COM= when writing mgf <2020-04-24 Fri>

Make writeMgfData example runnable <2020-04-20 Mon>
Fix issue when writing mgf with a connection (PR #505, by Rico Derks) <2020-04-20 Mon>
Add writeMgfData file/connection unit test <2020-04-20 Mon>

When reading MzTab files, the column names aren't converted to legal colnames (my make.names) - check.names in read.delim is now (internally) set to FALSE. This will make it easier to write MzTab objects back to files. See issue #501 for a discussion.
Re-introduce MzTab write support (contributed by Steffen Neumann). See #502.

Support reading of MzTab-M 2.0 format (contributed by Steffen Neumann).
Use UTF-8 encoding.

Fix failing unit test: in R 4.0, data.frames not don't cast strings to factors anymore <2020-03-24 Tue>

exprsToRatios is now defunct.

Need ProtGenerics 1.19.3 for impute generic

Need ProtGenerics 1.19.2
Deprecate filterZero and exprsToRatios

Bioconductor 3.11 (devel)

MSnbase 2.11

Fix bug in readSRMData (issue #486) which caused the function to not discriminate between chromatograms with different precursor collision energy.

Fix bug in pickPeaks: set variable centroided only to TRUE for spectra matching the provided msLevel..
Add parameter msLevel. to smooth.

Update news files titles to be consistent with other Bioc packages.

Updates to consensusSpectrum: add parameter mzFun allowing to define the aggregation function for m/z values, change default for mzd to 0 (hence avoid estimating m/z differences by default) and change the default for parameter intensityFun to median.

Use latest mzR

Update URL to point to pkgdown site

Add parameter weighted to consensusSpectrum and change the default from reporting the intensity-weighted mean of m/z values for consensus peaks to reporting the m/z of the largest peak <2019-09-12 Thu>.

Update to match changes in mzR version 2.17.4 <2019-09-04 Wed>.
Add parameter msLevel to pickPeaks to allow peak picking in specific MS levels. See #478 <2019-09-04 Wed>.

Use filterMsLevel,filterMz,filterPolarity,filterRt,filterAcquisitionNum,filterEmptySpectra,filterPrecursorScan,productMz,filterPrecursorMzandfilterIsolationWindowgenerics fromProtGenerics`.

plot,Spectrum,Spectrum now also supports MS1 spectra (see #477) <2019-07-23 Tue>

Make combineFeatures a method <2019-05-31 Fri>
Remove message about changed meaning of the "modifications" argument in calculateFragments' that was introduced in MSnbase 1.17.6 (2015-06-21). <2019-06-01 Sat>
Implement combineSpectra,MSnExp (see #474) <2019-06-02 Tue>.

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>.

Migrate generics to ProtGenerics

Bioconductor 3.10 (devel)

MSnbase 2.10

Bioconductor 3.9 (release)

MSnbase 2.9

remove plain NEWS file now that R supports NEWS.md

Add isolationWindowLowerMz and isolationWindowUpperMz methods <2019-04-15 Mon>
Add filterPrecursorMz method <2019-04-15 Mon>
Add filterIsolationWindow method <2019-05-16 Tue>

Remove NAnnotatedDataframe <2019-04-10 Wed>

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>

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>

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>

New version for Bioc 3.9 devel

MSnbase 2.8

New version for Bioc 3.8 release

MSnbase 2.7

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>

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)

Methods for Spectra class <2018-10-15 Mon>

Import rather than depend on BiocParallel <2018-10-15 Mon>
Fix failing test on Windows (requiring normalizePath) <2018-10-15 Mon>

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>

Fix unit tests (issue #360, wrong MS OBO CV terms for data smoothing (MS:1000592) and baseline correction (MS:1000593))

Fix wrong MS OBO CV terms for data smoothing (MS:1000592) and baseline correction (MS:1000593).

Add a note about parallel processing in vignette (see #356 for background) <2018-09-04 Tue>

Fix filterMz for spectra with no non-NA intensities in m/z range (see #355) <2018-08-08 Wed>

Fix bug in robust summary (see PR #349) <2018-07-28 Sat>
Fix failing unit test <2018-07-28 Sat>

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>

Version bump to force new vignette build

New devel version for Bioc 3.8

MSnbase 2.6

New release version for Bioc 3.7

MSnbase 2.5

Nothing yet.

Fix changed remote location of mzTab example files <2018-04-19 Thu>
Fix failing centroided unit test (see issue #338) <2018-04-20 Fri>

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>

Ensure tic and bpi with initial = TRUE calculate the tic and bpi from the data (related to issue #332). <2018-04-10 Tue>

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>

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>

New combineSpectra, combineSpectraMovingWindow, estimateMzScattering and estimateMzResulution functions <2018-03-05>.
New vignette describing profile mode data centroiding <2018-03-05>.

New as(MSnExp, data.frame) method <2018-02-16>
Speed up readMgfData function - see issue #319 <2018-03-13 Tue>

MSmap constructor for OnDiskMSnExp objects (see issue #305) <2018-01-31 Wed>
New filterMsLevel,MSnSet method <2018-02-06 Tue>

Fixing processing message when combining two MSnSets (reported by kamal.fartiyal84 https://support.bioconductor.org/p/100865/#105206) <2018-01-24 Wed>

Added TMT11-plex <2018-01-17 Wed>
Add phenoData<- method for pSet (issue #299 <2018-01-22>.
Change readMSnSet2 example <2018-01-23 Tue>

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>

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>

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>.

Update dependencies (see issue #271)
Replace HCD by ETD in TMT10ETD's name/description

New version for Bioc 3.7 (devel)

MSnbase 2.4

New version for Bioc 3.6 (release)

MSnbase 2.3

Use normalizePath to force absolute file paths in readMSData.

Add write support for MSnExp and OnDiskMSnExp objects allowing to save the MS data to mzML or mzXML files. <2017-09-15 Fri>

Keep protocolData in isobaric quantification; fixes #265

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).

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>

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>

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>.

export filterEmptySpectra

Brutally remove xic and chromatogram functions/methods, to be replaced by the Chromatogram[s] infrastructure <2017-06-15 Thu>

Fix superscript syntax in demo vignette <2017-06-14 Wed>

Use the injection time from mzR (see PR #109) which in now in seconds (was in milliseconds) <2017-06-13 Tue>

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>.

Rewrite utils.clean. It now keeps just the zeros in the direct neighbourhood (see #210) <2017-05-04 Thu>.

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)

Version bump for new Bioc devel.

MSnbase 2.2

Version bump for Bioc release version 3.5.

MSnbase 2.1

Set SerialParams() in an attempt to avoid random errors in tests - see issue #205 <2017-04-24 Mon>

suggest reshape2, as it's used in vignette <2017-04-18 Tue>

Update NEWS file <2017-04-11 Tue>

Remove timing test as it fails occasionally on the Bioconductor servers <2017-04-09 Sun>

Remove reshape2 dependency; see #201 <2017-04-06 Thu>

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>

Internal rewrite and speedup of plotNA <2017-02-26 Sun>

Import dist from stats <2017-02-25 Sat>
Fix filing example <2017-02-25 Sat>

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>

New diff.median normalisation for MSnSets. <2017-01-26 Thu>
Fix combineFeatures message <2017-02-01 Wed>

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>

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>)

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>

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>

Fix (unexported) navMS example code <2016-12-14 Wed>

Jo added netCDF support <2016-11-30 Wed>

FeaturesOfInterest collections can now be assigned names - addresses issue #172 <2016-11-25 Fri>

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>

Fix typo in impute man page <2016-10-19 Wed>
Cite Lazar 2016 in vignette imputation section <2016-10-28 Fri>

New version for Bioconductor devel

MSnbase 2.0.0

New version for Bioconductor release version 3.4

MSnbase 1.99

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>

Add removeReporters,OnDiskMSnExp (see issue #161 for details) <2016-10-07 Fri>

Fix bug in readMzTabData_v0.9 <2016-10-07 Fri>

Injection time is now added to the header when reading mzML files using readMSData2 (see issue #159) <2016-10-04 Tue>

Added isolationWindow,MSnExp method <2016-09-23 Fri>
Updated readMSData Spectrum2 class to support MS levels > 2 <2016-09-30 Fri>

Fix MS level test in quantify,OnDiskMSnExp to support MS2+ level quantitation <2016-09-14 Wed>

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

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>

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>

MSmap unit test <2016-05-23 Mon>
Fix bug in as(MSmap, "data.frame") <2016-05-23 Mon>

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>

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>

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>

Check for rownames/fnames in readMSnSet2 and unit test <2016-05-05 Thu>

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>

Version bump for new Bioc devel

MSnbase 1.20

Version bump for Bioc release version 3.3

MSnbase 1.19

more unit tests and bug fixes <2016-04-30 Sat> <2016-05-02 Mon>

more unit tests and bug fixes <2016-04-27 Wed> <2016-04-28 Thu>

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>

nadata.R unit tests and bugs fixed <2016-04-22 Fri>

Moved makeNaData[2] and whichNA (was in pRoloc) <2016-04-21 Thu>

new naplot function to visualise missing values as a heatmap and barplots along the samples and features. <2016-04-04 Mon>

fix typo in man <2016-04-02 Sat>

Write support of mzTab has been dropped (writeMzTabData, makeMTD, makePEP and makePRT are now defunct) <2016-03-18 Fri>

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>

limit readMSData unit test due to Windows-only error <2016-03-09 Wed>
fix unit test for utils.colSd(x, na.rm=TRUE)

Document change in nQuants param fcol to groupBy <2016-03-02 Wed>

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>

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>

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>

export exprs, fvarLabels, and sampleNames[<-] <2016-01-30 Sat>

new trimws method for data.frames and MSnSets <2016-01-29 Fri>

readMSnSet2 now also accepts a data.frame as input <2016-01-29 Fri>
selective ggplot2 import <2016-01-29 Fri>

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>

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>

Merged pull request #67 from lgatto/featureCV by sgibb: featureCV ignores its na.rm argument <2015-12-12 Sat>

Replacement method for MSnSetList names <2015-11-24 Tue>

New argument fcol to selectFeatureData to select feature variables using a vector <2015-10-28 Wed>

new selectFeatureData function to subset the feature data <2015-10-24 Sat>

Remove generics that are defined in ProtGenerics <2015-10-15 Thu>

Bioc devel 3.3

MSnbase 1.18

Bioc release 3.2

MSnbase 1.17

new default parameter 'feature weight' in iPQF by Martina Fisher (see PR#65) <2015-10-07 Wed>

Fix typo in plot man <2015-08-23 Sun>

Fix typo in impute man <2015-08-17 Mon>

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>

fix show MIAPE when some otherInfo at NA <2015-07-15 Wed>

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>

Fix URL <2015-06-30 Tue>

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>

coercion from IBSpectra to MSnSet, as per user request <2015-06-23 Tue>
new iPQF combineFeature method <2015-06-24 Wed>

Fix support of identification-only mzTab files <2015-06-22 Mon>

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>

new MzTab class to store a simple parsing of an mzTab version 1 data file. See ?MzTab for details. <2015-06-16 Tue>

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>

iTRAQ 8-plex correction factors and impurity matrix <2015-05-22 Fri>

new filterZero function <2015-05-01 Fri>

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>

new devel version for Bioc 3.2

MSnbase 1.15

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]

add TMT10 paragraph and fig to demo vignette [2015-04-09 Thu]

support for TMT10 plex [2015-04-08 Wed]

using serial parallelisation during quantitation in unit tests [2015-04-02 Thu]

new msnset data, used in various examples instead of quantifying the itraqdata experiment over and over again [2015-04-01 Wed]

improve nbavg imputation description and add example [2015-03-22 Sun]
reduce compareSpectra example timing [2015-03-30 Mon]

average neighbour imputation for ordered fractions along a gradient [2015-03-21 Sat]

update malformed Description [2015-03-20 Fri]

update compareSpectra man [2015-03-19 Thu]
ExpressionSet <-> MSnSet coercion [2015-03-19 Thu]

use S4Vectors' isEmpty generic [2015-03-10 Tue]

Improved imputation section in demo vignette [2015-03-05 Thu]

Importing ProtGenerics [2015-02-28 Sat]
selective import of MALDIquant [2015-03-02 Mon]

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]

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]

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]

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]

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]

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]

Devel version for Bioc 3.1

MSnbase 1.14

Release version for Bioc 3.0

MSnbase 1.13

width generic if non-existant [2014-09-03 Wed]
fix undocumented S4 methods warnings [2014-09-27 Sat]

msMap(MSmap)<- method [2014-08-12 Tue]
Typo in MIAPE man [2014-08-29 Fri]

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]

fix issue with readMSnSet2 without fdata [2014-07-28 Mon]

Don't import width from IRanges [2014-07-23 Wed]
qual slot is populated again [2014-07-23 Wed]

remove Vennerable::Venn from example and DESCRIPTION [2014-06-19 Thu]

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]

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]

Add recommended biocView [2014-06-05 Thu]

Bug tracking link [2014-05-26 Mon]

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]

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]

Document difference between traceable and non-traceable FeaturesOfInterest instances [2014-04-30 Wed]
ignoring desciptions with length > 1 [2014-04-30 Wed]

FeaturesOfInterest [2014-04-29 Tue]

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]

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]

New devel version for Bioc 3.0

MSnbase 1.11

update dependency to R >= 3.1 [2014-04-05 Sat]

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]

Fixed a bug in readMzTabData reported by Hendrik Weisser [2014-03-26 Wed]

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]

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]

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]

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]

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]

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]

passing ... to sweep when normalising [2013-12-08 Sun]
updated makeMTD to accomodate new MS ontology [2013-12-23 Mon]

updated mzTab example files to new url [2013-11-15 Fri]
warning about mzTab versions [2013-11-15 Fri]

move inst/doc to vignettes [2013-10-19 Sat]

document na.rm in combineFeatures Rd [2013-10-18 Fri]

New devel version for Bioc 2.14

MSnbase 1.9

fix MSnSet -] ExpressionSet [2013-10-13 Sun]
MSnSet -] ExpressionSet unit test [2013-10-13 Sun]

MIAPE to MIAME conversion [2013-10-11 Fri]
proper MIAME when MSnSet -] ExpressionSet [2013-10-11 Fri]

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]

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]

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]

Passing ... to read.table in MSnbase:::readIspy[Silac|15N]Data [2013-09-16 Mon]
QualityControl biocView [2013-09-16 Mon]

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]

typo in Author[s]@R [2013-05-15 Wed]

new simple MSnSet constructor [2013-05-07 Tue]

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]

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]

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]

new Bioc 2.13 devel version

MSnbase 1.8

new Bioc 2.12 stable version

MSnbase 1.7

updated itraqdata to fix issue in vignette when combine(exp1, exp2) and different MIAPE versions [2013-03-22 Fri]

Mention scale in vignette [2013-03-02 Sat]
exprsToRatio matrix method [2013-03-20 Wed]

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]

msnbase.r na.rm arg [2013-02-20 Wed]

Added impute method [2013-02-19 Tue]

Explicitating that normalise and normalize are the same methods in the man. [2013-02-13 Wed]

adding MIAPE and pSet accessors: analyserDetails, analyzerDetails, ionSourceDetails, instrumentModel, instrumentManufacturer, instrumentCustomisations [2013-02-12 Tue]
switching back to analyserDetails slot [2013-02-12 Tue]

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]

added a analyzer accessors/slot to accomodate new mzTab files with more meta-data [2013-01-30 Wed]

fixing knitr 1.0 compatibility [2013-01-15 Tue]

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]

new unexported readIspy15NData [2013-01-09 Wed]
min.int readIspy[Silac|15N]Data arg [2013-01-11 Fri]

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]

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]

new 'pattern' argument to filterNA [2012-12-15 Sat]
vignette and man updates [2012-12-15 Sat]
filterNA(, pattern) tests [2012-12-15 Sat]

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]

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]

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]

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]

Fixed bug in readIspyData, reported by Claire Mulvey [2012-11-27 Tue]

dropping levels in readIspySilacData [2012-11-06 Tue]
fixed plotNA [2012-11-09 Fri]

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]

updating readMzTabData to properly capture experiment description [2012-10-12 Fri]

fixed readMSData for MS1 [2012-10-08 Mon]

fixed vignettes [2012-10-02 Tue]

Version bump for next devel release [2012-10-01 Mon]

MSnbase 1.5

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]

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]

updated quantify documentation [2012-09-24 Mon]
changed all foo.class functions to foo_class [2012-09-24 Mon]

setting parallel default to FALSE [2012-09-22 Sat]
enhanced parallel in DESCRIPTION and detectCores() passed to registerDoMC [2012-09-23 Sun]

removed registerDoMC no visible global function NOTE [2012-09-21 Fri]
fixed NOTE about xvarname which was a bug [2012-09-21 Fri]

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]

updated all ReporterIons rda data [2012-09-13 Thu]
Using && in testing parallel, require(foreach and doMC) [2012-09-14 Fri]

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]

changed TMT7[7] mass from 229.26 to 230.17 and ReporterIons descriptions [2012-09-12 Wed]

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]

updating code to ggplot2 v0.9.2 [2012-09-07 Fri]

added platform test to use doMC (d.tenenbaum) [2012-08-31 Fri]

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]

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]

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]

Fixed readMSData instrumentInfo handling (reported by Gopuraja Dharmalingam) [2012-06-05 Tue]
new multiple file loading test in test_io [2012-06-05 Tue]

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]

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]

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]

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]

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]

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]

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]

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]

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]

new devel version bump

MSnbase 1.3

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

new is.na.MSnSet [2012-02-16 Thu]
updated vignette and NA related man pages with cross-links [2012-02-16 Thu]

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]

new topN methods + doc + tests [2012-02-14 Tue]

changed explicit close(file) in writeMgf methods to on.exit(close(file)) [2012-02-12 Sun]
typo in vignette [2012-02-13 Mon]

type in writeMgfData man [2012-02-07 Tue]
updated TITLE in writeMgfData [2012-02-08 Wed]

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]

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]

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]

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]

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]

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]

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]

\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]

Herve added BioGenerics as a dependency and import statement in NAMESPACE [2011-11-29 Tue]

Version bump for Bioc 2.10 devel

MSnbase 1.2

Version bump for Bioc 2.9 release

MSnbase 1.1

added pgfSweave to Suggests [2011-10-23 Sun]

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]

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]

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]

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]

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]

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]

updated write.exprs to add fData columns [2011-09-08 Thu]
added write.exprs and readMSnSet unit test [2011-09-08 Thu]

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]

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]

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]

added addVigs2WinMenu call in .onAttach [2011-06-26 Sun]
added plotMzDelta paragraph in vignette [2011-06-26 Sun]

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]

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

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]

added invisible(NULL) to all show methods [2011-06-08 Wed]
added centroided argument to plot.MSnExp [2011-06-09 Thu]

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]

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]

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]

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]

reporter ions purity correction method, man and test [2011-05-09 Mon]
updated vignette [2011-05-09 Mon]

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]

added combineFeatures example in demo vignette [2011-05-05 Thu]

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]

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]

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]

added setAs data.frame and as.data.frame methods for Spectrum objects [2011-03-29 Tue]
support for uncentroided MS2 spectra plots [2011-03-31 Thu] [2011-04-02 Sat]
support for uncentroided MS1 spectra plots [2011-04-02 Sat]
minor modification to readIspyData [2011-04-04 Mon]
removed centroided slot from MSnProcess and added to individial Spectrum instances. Relevant for Velos HCD (profile)/CID (uncentroided) data [2011-04-04 Mon]
modified readMzXmlData accordingly [2011-04-04 Mon]
added validObject(new(...)) tests for each class [2011-04-04 Mon]
added centroided[<-] methods to Spectrum and pSet [2011-04-04 Mon]
added 'keepAll' parameter to readIspyData [2011-04-11 Mon]

MSnbase 0.99

removed pgfSweave from Suggests field [2011-04-04 Mon]

Using Sweave rather than pgfSweave to build on lamb1. [2011-03-28 Mon]

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]

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]

MSnProcess@process get's one line when subsetting and MSnExp object [2011-03-21 Mon]
Updated vignette Makefile [2011-03-22 Tue]
Added fake vignettes [2011-03-22 Tue]
Version set to 0.99.0 [2011-03-22 Tue]
Minor changes in quantify-method.Rd [2011-03-22 Tue]
added .Rbuildignore to ignore 'sweave-cache.*' [2011-03-22 Tue]
added R/zzz.R with start-up message [2011-03-23 Wed]
Added width generic [2011-03-23 Wed]
IRanges in now imported [2011-03-23 Wed]

MSnbase 0.2

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.

MSnbase 0.1

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.

added pgfSweave to Suggests, as is called in vignette Makefile

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

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")

Added LazyLoad: yes in DESCRIPTION and modified docs accordingly
Added NEWS file

Added MSnbase-demo vignette
Added MSnbase-development vignette

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.

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lgatto/MSnbase Base Functions and Classes for Mass Spectrometry and Proteomics

NEWS.md In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase 2.33

MSnbase 2.33.2

MSnbase 2.33.1

MSnbase 2.33.0

MSnbase 2.31

MSnbase 2.31.1

MSnbase 2.31.0

MSnbase 2.29

MSnbase 2.29.4

MSnbase 2.29.3

MSnbase 2.29.2

MSnbase 2.29.1

MSnbase 2.29.0

MSnbase 2.27

MSnbase 2.27.1

MSnbase 2.27.0

MSnbase 2.25

MSnbase 2.25.2

MSnbase 2.25.1

MSnbase 2.25.0

MSnbase 2.24

MSnbase 2.24.0

MSnbase 2.23

Changes in 2.23.2

Changes in 2.23.1

Changes in 2.23.0

MSnbase 2.22

Changes in 2.22.0

MSnbase 2.21

Changes in 2.21.7

Changes in 2.21.6

Changes in 2.21.5

Changes in 2.21.4

Changes in 2.21.3

Changes in 2.21.2

Changes in 2.21.1

MSnbase 2.19

Changes in 2.19.2

Changes in 2.19.1

MSnbase 2.17

Changes in 2.17.8

Changes in 2.17.7

Changes in 2.17.6

Changes in 2.17.5

Changes in 2.17.4

Changes in 2.17.3

Changes in 2.17.2

Changes in 2.17.1

Changes in 2.17.0

MSnbase 2.15

Changes in 2.15.7

Changes in 2.15.6

Changes in 2.15.5

Changes in 2.15.4

Changes in 2.15.3

Changes in 2.15.2

Changes in 2.15.1

Changes in 2.15.0

MSnbase 2.14

Changes in 2.14.0

MSnbase 2.13

Changes in 2.13.9

Changes in 2.13.8

Changes in 2.13.7

Changes in 2.13.6

Changes in 2.13.5

Changes in 2.13.4

Changes in 2.13.3

Changes in 2.13.2

Changes in 2.13.1

Changes in 2.13.0

MSnbase 2.11

Changes in 2.11.13

Changes in 2.11.12

Changes in 2.11.11

Changes in 2.11.10

Changes in 2.11.9

Changes in 2.11.8

lgatto/MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics

NEWS.md
In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics