MSnbase 2.15

Changes in 2.15.7

  • Nothing yet

Changes in 2.15.6

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

Changes in 2.15.5

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

Changes in 2.15.4

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

Changes in 2.15.3

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

Changes in 2.15.2

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

Changes in 2.15.1

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

Changes in 2.15.0

  • Bioconductor devel version (Bioc 3.12)

MSnbase 2.14

Changes in 2.14.0

  • Bioconductor release version (Bioc 3.11)

MSnbase 2.13

Changes in 2.13.9

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

Changes in 2.13.8

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

Changes in 2.13.7

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

Changes in 2.13.6

  • When reading MzTab files, the column names aren’t converted to legal colnames (my make.names) - check.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.

Changes in 2.13.5

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

Changes in 2.13.4

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

Changes in 2.13.3

  • exprsToRatios is now defunct.

Changes in 2.13.2

  • Need ProtGenerics 1.19.3 for impute generic

Changes in 2.13.1

  • Need ProtGenerics 1.19.2
  • Deprecate filterZero and exprsToRatios

Changes in 2.13.0

  • Bioconductor 3.11 (devel)

MSnbase 2.11

Changes in 2.11.13

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

Changes in 2.11.12

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

Changes in 2.11.11

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

Changes in 2.11.10

  • 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.

Changes in 2.11.9

  • Use latest mzR

Changes in 2.11.8

  • Update URL to point to pkgdown site

Changes in 2.11.7

  • 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>.

Changes in 2.11.6

  • 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>.

Changes in 2.11.5

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

Changes in 2.11.4

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

Changes in 2.11.3

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

Changes in 2.11.2

  • 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 2.11.1

  • Migrate generics to ProtGenerics

Changes in 2.11.0

  • Bioconductor 3.10 (devel)

MSnbase 2.10

Changes in 2.10.0

  • Bioconductor 3.9 (release)

MSnbase 2.9

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

MSnbase 2.8

Changes in version 2.8.0

  • New version for Bioc 3.8 release

MSnbase 2.7

Changes in version 2.7.12

  • Fix warnings on windows (see #371) <2018-10-26 Fri>
  • Add parameter ppm to consensusSpectrum and meanMzInts (see #373 for details) <2018-10-26 Fri>

Changes in version 2.7.11

  • Change default for timeDomain in combineSpectra and combineSpectraMovingWindow to FALSE <2018-10-18 Thu>
  • Add new spectra combination function consensusSpectrum <2018-10-24 Wed>
  • Amend plot,Spectrum 1 and 2 (see #369)

Changes in version 2.7.10

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

Changes in version 2.7.9

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

Changes in version 2.7.8

  • MGF exporter gets a new addFields argument (see PR #362) <2018-10-12 Fri>
  • New Spectra (SimpleList of Sepctrum objects) (see PR #361) <2018-10-13 Sat>

Changes in version 2.7.7

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

Changes in version 2.7.6

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

Changes in version 2.7.5

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

Changes in version 2.7.4

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

Changes in version 2.7.3

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

Changes in version 2.7.2

  • Handle files without any spectra - see #342 <2018-05-15 Tue>
  • New mergeFeatureVars and expandFeatureVars functions <2018-05-30 Wed>
  • Update plot,Spectrum methods to match the tolerance and relative arguments (see #350) <2018-06-29 Fri>

Changes in version 2.7.1

  • Version bump to force new vignette build

Changes in version 2.7.0

  • New devel version for Bioc 3.8

MSnbase 2.6

Changes in version 2.6.0

  • New release version for Bioc 3.7

MSnbase 2.5

Changes in version 2.5.15

  • Nothing yet.

Changes in version 2.5.14

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

Changes in version 2.5.13

  • Reduce unit testing time (see #334) <2018-04-13 Fri>
  • Fix bug in write.exprs when only one feature data is passed <2018-04-17 Tue>

Changes in version 2.5.12

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

Changes in version 2.5.11

  • Improve combineFeatures manual to document the effect for missing values for different types of aggregation methods <2018-04-07 Sat>
  • Update robust summary to hangle missing values (see #330). <2018-04-09 Mon>

Changes in version 2.5.10

  • New robust summarisation method in combineFeatures contributed by Ludger Goeminne, Adriaan Sticker and Lieven Clement <2018-04-03 Tue>
  • Adapt utils.removePeaks to new IRanges implementation; thanks to H. Pagès for the implementation (see PR #320 for discussion) <2018-03-26>.
  • Centroiding information is retrieved from raw files (for mzML/mzXML files;. see issue #325 <2018-03-27>
  • Add parameter timeDomain to combineSpectra, combineSpectraMovingWindow and estimateMzScattering allowing to perform the grouping of m/z values from consecutive scans based on the square root of the m/z values <2018-03-29>.
  • Assure feature CV feature variable names are unique when combining feature repeatedly (see issue #303) <2018-04-04 Wed>

Changes in version 2.5.9

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

Changes in version 2.5.8

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

Changes in version 2.5.7

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

Changes in version 2.5.6

Changes in version 2.5.5

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

Changes in version 2.5.4

  • Add featureData slot to Chromatograms class and add mz, precursorMz and productMz methods for Chromatograms (issue #289) <2017-12-18 Mon>.
  • Add readSRMData function to read chromatographic data from SRM (MRM) experiments; issue #286 <2018-01-10 Wed>.
  • The MSnSetList class has a new featureData slot, accessible with fData to store metadata for the individial MSnSets of the list. MSnSetList also not has an sapply method. <2018-01-10 Wed>
  • combineFeatures now has a new fcol argument (see issue #195) <2018-01-11 Thu>

Changes in version 2.5.3

  • Add filterPrecursorScan for MSnExp and OnDiskMSnExp; closes issue #282 and PR #287 <2017-12-16 Sat>.
  • MSnSet to/from SummarizedExperiment coercion (contributed by Arne Smits in PR #284) <2017-12-17 Sun>
  • Fix inverted M/Z axis in plot3D,MSmap (reported by Sylvain Dechaumet, see issue #292) <2017-12-19 Tue>

Changes in version 2.5.2

  • Use automatic backend detection (based on file name and file content) that was introduced in mzR version 2.13.1 (issue #275).
  • Fix mzML file writing unit tests to work with recently introduced header column “filterString” (issue #278).
  • Reduce number of comparsions in in internal fastquant_max to get little speed improvents for isobaric quantification (see PR #280) <2017-11-27 Mon>.
  • MIAxE, MSnProcess and AnnotatedDataFrame coercion to list methods (in related to PR #280) <2017-12-11 Mon>
  • Add support to reduce the featureData for OnDiskMSnExp objects (issue #285) <2017-12-11 Mon>.

Changes in version 2.5.1

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

Changes in version 2.5.0

  • New version for Bioc 3.7 (devel)

MSnbase 2.4

Changes in version 2.4.0

  • New version for Bioc 3.6 (release)

MSnbase 2.3

Changes in version 2.3.14

  • Use normalizePath to force absolute file paths in readMSData.

Changes in version 2.3.13

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

Changes in version 2.3.12

  • Keep protocolData in isobaric quantification; fixes #265

Changes in version 2.3.11

  • Amend addIdentificationData when sourceInfo reports multiple files and when scores are missing from the identification results (closes #261).
  • Don’t overwrite processingData slot when creating an MSnSet object (closes #264).

Changes in version 2.3.10

  • New isCentroidedFromFile function <2017-08-11 Fri>
  • Add msLevel slot to Chromatogram object <2017-08-16 Wed>
  • Add msLevel argument to chromatogram,MSnExp method <2017-08-16 Wed>
  • calculateFragments now just calculate fragments for all n - 1L bonds (before it incorrectly adds an additional bond; fixes #248) <2017-08-20 Sun>
  • Add isEmpty methods for Chromatogram and Chromatograms objects <2017-09-05 Tue>
  • plot,Chromatogram[s] creates an empty plot and returns a warning if the Chromatogram[s] object is empty (issue #249) <2017-09-05 Tue>

Changes in version 2.3.9

  • Using new mzR::openIdfile backend to add identifcation data to raw and quantitative data (see issue #232) <2017-07-28 Fri>
  • New utils functions: factorsAsStrings, makeCamelCase and reduce,data.frame <2017-07-29 Sat>
  • Coerce mzRident to data.frames <2017-07-29 Sat>
  • Add phenoData slot to Chromatograms class<2017-08-02 Wed>
  • new readMzIdData function to read mzId files as data.frames (uses the new coerce,mzRident,data.frame method) <2017-08-03 Thu>
  • new filterIdentificationDataFrame function to filter PSM data.frames as produced by readMzIdData. Also used in the addIdentificationData methods. <2017-08-03 Thu>
  • readMSData has a new mode argument to set onDisk or inMemory (default) mode <2017-08-10 Thu>

Changes in version 2.3.8

  • New infrastructure for chromatogram data <2017-06-24 Sat>
  • Change naming scheme for spectra: FFILEID.SSPECTRUMID, e.g. F01.S0001. Before it has been XSPECTRUMID.FILEID. The new naming scheme changes the order of the spectra. See #255 (and PR #256) for details <2017-06-25 Sun>.

Changes in version 2.3.7

  • export filterEmptySpectra

Changes in version 2.3.6

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

Changes in version 2.3.5

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

Changes in version 2.3.4

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

Changes in version 2.3.3

  • Rewrite getColsFromPattern and getRowsFromPattern and add unit tests <2017-05-11 Thu>.
  • Add .filterNA and rewrite filterNA for matrix and MSnSet <2017-05-11 Thu>.
  • Convert main MSnbase-demo vignette to Rmd/html <2017-05-27 Sat>
  • naplot gains a reorderRows and reorderColumns argument <2017-06-05 Mon>.

Changes in version 2.3.2

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

Changes in version 2.3.1

  • Introduce “NTR” method for combineFeatures <2017-04-26 Wed>.
  • Rewrite nQuants and featureCV to avoid returning of rows for empty factors; see PR #208 for details <2017-04-28 Fri>.
  • Add $,pSet method to easily access columns in the phenoData (see #203)

Changes in version 2.3.0

  • Version bump for new Bioc devel.

MSnbase 2.2

Changes in version 2.2.0

  • Version bump for Bioc release version 3.5.

MSnbase 2.1

Changes in version 2.1.19

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

Changes in version 2.1.18

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

Changes in version 2.1.17

  • Update NEWS file <2017-04-11 Tue>

Changes in version 2.1.16

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

Changes in version 2.1.15

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

Changes in version 2.1.14

  • Internal rewrite and speedup of topN; Briefly multiple apply calls are avoided, getTopIdx and subsetById are replaced by .topIdx. See PR #199 for details. <2017-03-20 Mon>
  • Fix mz calculation for terminal modifications and z > 1 in calculateFragments; closes #200 <2017-03-22 Wed>
  • Fix errors and notes <2017-03-30 Thu>

Changes in version 2.1.13

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

Changes in version 2.1.12

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

Changes in version 2.1.11

  • Fix breaks calculation for binning single (closes #191) and multiple (closes #190) spectra. The fix for single spectra (#191) could result in slightly different breaks on the upper end of the m/z values. <2017-02-10 Fri>
  • New aggvar function, to assess aggregation variability <2017-02-11 Sat>

Changes in version 2.1.10

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

Changes in version 2.1.9

Changes in version 2.1.8

  • Remove order option altogether <2017-01-19 Thu> (superseeds setting default sorting using “auto” on R < 3.3 and “radix” otherwise <2017-01-03 Tue>)

Changes in version 2.1.7

  • Setting default sorting using “auto” on R < 3.3 and “radix” otherwise <2017-01-03 Tue>
  • filterMz returns an empty spectrum when no data is within the mz range (see issue #181) <2017-01-16 Mon>
  • Performance improvement: a new private .firstMsLevel will efficiently return the first MS level in an MSnExp and OnDiskMSnExp. See issue #183 for details/background <2017-01-18 Wed>

Changes in version 2.1.6

  • Migrate io and dev vignettes to BiocStyle’s html_document2 style <2016-12-23 Fri>
  • Update show method to display class.
  • Migrated to NEWS.md <2016-12-23 Fri>
  • Update DESCRIPTION (and README) to reflect wider usage of MSnbase (replaced MS-based proteomics by mass spectrometry and proteomics) <2016-12-23 Fri>

Changes in version 2.1.5

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

Changes in version 2.1.4

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

Changes in version 2.1.3

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

Changes in version 2.1.2

  • Update readMSnSet2 to save filename <2016-11-09 Wed>
  • Ensure that header information is read too if spectra data is loaded for onDiskMSnExp objects (see issue #170) <2016-11-24 Thu>

Changes in version 2.1.1

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

Changes in version 2.1.0

  • New version for Bioconductor devel

MSnbase 2.0.0

  • New version for Bioconductor release version 3.4

MSnbase 1.99

Changes in version 1.99.6

  • Reverting to old initialize,Spectrum (see issue #163) <2016-10-07 Fri>
  • Setting Spectrum class versions outside of prototype (see issue #163). For this, there is now a vector of class version in .MSnbaseEnv <2016-10-10 Mon>

Changes in version 1.99.5

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

Changes in version 1.99.4

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

Changes in version 1.99.3

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

Changes in version 1.99.2

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

Changes in version 1.99.1

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

Changes in version 1.99.0

  • Add normalize method for onDiskMSnExp <2016-06-07 Tue>.
  • Fix bug in readMSData <2016-06-07 Tue>.
  • Added documentation and unit test for trimMz <2016-06-01 Wed>.
  • Added trimMz method for onDiskMSnExp objects <2016-05-31 Tue>.
  • Added (internal) method spectrapply to apply a function to all spectra of an onDiskMSnExp object; does the data import, subsetting, application of lazy processing steps etc. <2016-05-27 Fri>.
  • Added a section to the MSnbase-development vignette <2016-05-27 Fri>.
  • Finished with all pSet inherited methods and docs <2016-05-26 Thu>.
  • Added rtlim argument to spectra method for onDiskMSnExp <2016-05-26 Thu>.
  • Methods rtime, tic, ionCount, polarity and acquisitionNum implemented <2016-05-25 Wed>.
  • Documentation added for most methods <2016-05-25 Wed>.
  • Methods peaksCount and spectra for onDiskMSnExp objects implemented <2016-05-24 Tue>.
  • Performance and validation tests for the Spectrum1 C-constructor <2016-05-23 Mon>.
  • Spectrum1 constructor implemented in C (presently not exported) <2016-05-20>
  • length, scanIndex, acquisitionNum and centroided implemented <2016-05-20>
  • Implemented fromFile and msLevel for onDiskMSnExp <2016-05-19 Thu>
  • Implemented an onDiskMSnExp class for on-the-fly data import <2016-05-19 Thu>
  • Fixed the validate method for pSet to play nicely with onDiskMSnExp objects <2016-05-19 Thu>
  • Added slot onDisk to pSet objects (TRUE for onDiskMSnExp objects, FALSE otherwise). The getter method isOnDisk checks for the presence of the slot in the object (backward compatibility) <2016-05-19 Thu>
  • Implemented a ProcessingStep class that helps to keep track how (spectra) data should be processed on the fly <2016-05-18 Wed>
  • In onDiskMSnExp validity, check that the assaydata is empty <2016-06-28 Tue>
  • Pass neutralLoss in plot,Spectrum,Spectrum-method to .calculateFragments; fixes #146 <2016-08-12 Fri>
  • Allow the user to specify the cex, lwd, pch for peaks and fragments in plot,Spectrum,Spectrum-method; closes #148 <2016-08-12 Fri>
  • Update centroided with an na.fail argument (see issue #150 for details) <2016-08-12 Fri>
  • Fix warning in readMgfData if TITLE contains multiple “=” <2016-08-24 Wed>

MSnbase 1.21

Changes in version 1.21.8

  • Update MSnSet validity method to guard agains empty string feature names <2016-06-20 Mon>
  • Simplify show,MSnExp method to work for various MS level cases and onDiskMSnExp - addressed issue #98 <2016-06-28 Tue>
  • removeMultipleAssignment also removes features that were not assigned (i.e. that have fcol (nprots) NA) <2016-07-02 Sat>
  • New smoothed slot/accessor/replacement methods <2016-07-08 Fri>
  • Update reporter masses and add TMT10 ETD/HCD <2016-07-20 Wed>
  • returning empty spectrum when fliterMz has empty range - see issue #134 <2016-07-22 Fri>
  • (mz, intensity) values are reordered based on order(mz) - see issue #135 <2016-07-26 Tue>
  • fix bug in bin,Spectrum - see issue #137 <2016-08-05 Fri>

Changes in version 1.21.7

  • Update iPQF reference <2016-06-01 Wed>
  • Fix a bug in normalize method for MSnExp objects: assigning normalized spectra directly to assayData is not possible, as the environment is locked. See PR #91.
  • readMSData: if no phenodata is provided it creates an empty one with rownames corresponding to the file names. See PR #91.
  • Lock itraqdata’s assaydata bindings <2016-06-08 Wed>

Changes in version 1.21.6

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

Changes in version 1.21.5

  • Added Johannes as contributor <2016-05-12 Thu>
  • Deprecate MzTab v0.9 <2016-05-19 Thu>
  • Fix old googlecode URLs to old MzTab <2016-05-19 Thu>

Changes in version 1.21.4

  • More MzTab and Spectrum1 unit testing <2016-05-08 Sun>
  • Speed up readMSData (PR #86 by jotsetung) <2016-05-12 Thu>
  • Replace example file URL to use github instead of googlecode <2016-05-12 Thu>

Changes in version 1.21.3

  • No fileNames replacement method <2016-05-07 Sat>
  • fileNames unit tests <2016-05-07 Sat>
  • add fileNames to class that had fileName accessor (MSmap, MzTab) <2016-05-07 Sat>

Changes in version 1.21.2

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

Changes in version 1.21.1

  • Fix wrong indexing in readMSdata, msLevel==1 (PR #85 by jotsetung) <2016-05-04 Wed>
  • grep/getEcols have a ‘n’ param specifying which line to grep/get <2016-05-04 Wed>

Changes in version 1.21.0

  • Version bump for new Bioc devel

MSnbase 1.20

Changes in version 1.20.0

  • Version bump for Bioc release version 3.3

MSnbase 1.19

Changes in version 1.19.24

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

Changes in version 1.19.23

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

Changes in version 1.19.22

  • more unit tests <2016-04-23 Sat> <2016-04-24 Sun> <2016-04-26 Tue>
  • remove readIspyData functions <2016-04-23 Sat>
  • Fixed bug in error catching in utils.mergeSpectraAndIdentificationData <2016-04-23 Sat>

Changes in version 1.19.21

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

Changes in version 1.19.20

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

Changes in version 1.19.19

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

Changes in version 1.19.18

  • fix typo in man <2016-04-02 Sat>

Changes in version 1.19.17

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

Changes in version 1.19.16

  • add estimateNoise,[Spectrum|MSnExp]-method; closes #78 <2016-03-10>
  • import a lot of functions from recommended packages, namely graphics, stats and utils to avoid many “Undefined global functions or variables” NOTEs in R CMD check <2016-03-10>

Changes in version 1.19.15

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

Changes in version 1.19.14

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

Changes in version 1.19.13

  • Fixed bug in bin_Spectrum, reported by Weibo Xie <2016-02-16 Tue>
  • Added unit test for bug above <2016-02-16 Tue>
  • Merged ‘apply functions columnwise by group’ <2016-02-16 Tue>
  • In nQuants, the fcol argument has been replaced with groupBy to make the signature consistent with featureCV <2016-02-16 Tue>

Changes in version 1.19.12

  • Moved polarity slot from Spectrum1 (0.1.0 -> 0.2.0) to Spectrum (0.2.0 -> 0.3.0) superclass; also bumped Spectrum2 class (0.1.0 -> 0.2.0) and MSnExp (0.3.0 -> 0.3.1, to trace changes in Spectrum2). Wrote MSnExp and Spectrum2 updateObject methods. <2016-02-11 Thu>

Changes in version 1.19.11

  • Fix trimws generic/methods with useAsDefault (see issue #75) <2016-02-02 Tue>
  • add exprs,MSnSet-method alias (since exprs is now exported) <2016-02-02 Tue>

Changes in version 1.19.10

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

Changes in version 1.19.9

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

Changes in version 1.19.8

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

Changes in version 1.19.7

  • new sampleNames<- for pSet and MSnExp objects <2015-12-15 Tue>
  • Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat) <2015-12-18 Fri>

Changes in version 1.19.6

  • MSnExp feautreNames are now X01, X02 (0 after X) to maintain numerical sorting of ASCII characters; contributed by sgibb <2015-12-14 Mon>
  • Update MSnbase:::subsetBy to use split instead of lapply, which makes topN faster. This nevertheless changes the order of the resulting MSnSet (see issue #63 for details and background); contributed by sgibb <2015-12-14 Mon>

Changes in version 1.19.5

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

Changes in version 1.19.4

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

Changes in version 1.19.3

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

Changes in version 1.19.2

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

Changes in version 1.19.1

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

Changes in version 1.19.0

  • Bioc devel 3.3

MSnbase 1.18

Changes in version 1.18.0

  • Bioc release 3.2

MSnbase 1.17

Changes in version 1.17.16

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

Changes in version 1.17.15

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

Changes in version 1.17.14

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

Changes in version 1.17.13

  • partly rewrite writeMgfData <2015-05-16 Thu>
  • initial hmap function <2015-07-16 Thu>
  • fix bug in plotting MS1 spectra (closes issue #59) <2015-07-16 Thu>
  • new image implementation, based on @vladpetyuk’s vp.misc::image_msnset <2015-07-25 Sat>
  • Changed the deprecated warning to a message when reading MzTab data version 0.9, as using the old reader can not only be achived by accident and will be kept for backwards file format compatibility <2015-07-30 Thu>

Changes in version 1.17.12

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

Changes in version 1.17.11

  • adding unit tests <2015-07-01 Wed>
  • fix abundance column selection when creating MSnSet form MzTab <2015-07-01 Wed>
  • new mzTabMode and mzTabType shortcut accessors for mode and type of an mzTab data <2015-07-01 Wed>

Changes in version 1.17.10

  • Fix URL <2015-06-30 Tue>

Changes in version 1.17.9

  • calculateFragments’ “neutralLoss” argument is now a list (was a logical before), see #47. <2015-06-24 Wed>
  • add defaultNeutralLoss() function to fill calculateFragments’ modified “neutralLoss” argument, see #47. <2015-06-24 Wed>

Changes in version 1.17.8

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

Changes in version 1.17.7

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

Changes in version 1.17.6

  • Export metadata,MzTab-method <2015-06-19 Fri>
  • Replace spectra,MzTab-method by psms,MzTab-method <2015-06-20 Sat>
  • Change the meaning of calculateFragments’ “modifications” argument. Now the modification is added to the mass of the amino acid/peptide. Before it was replaced. <2015-06-21 Sun>
  • calculateFragments gains the feature to handle N-/C-terminal modifications, see #47. <2015-06-21 Sun>
  • update readMzTabData example <2015-06-22 Mon>

Changes in version 1.17.5

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

Changes in version 1.17.4

  • New lengths method for FoICollection instances <2015-06-06 Sat>
  • New image2 function for matrix object, that behaves like the method for MSnSets <2015-06-10 Wed>
  • image,MSnSet labels x and y axis as Samples and Features <2015-06-10 Wed>
  • fixed bug in purityCorrect, reported by Dario Strbenac <2015-06-11 Thu>

Changes in version 1.17.3

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

Changes in version 1.17.2

  • new filterZero function <2015-05-01 Fri>

Changes in version 1.17.1

  • new MSnSetList class <2015-04-19 Sun>
  • new commonFeatureNames function <2015-04-14 Tue>
  • new compareMSnSets function <2015-04-19 Sun>
  • splitting and unsplitting MSnSets/MSnSetLists <2015-04-19 Sun>

Changes in version 1.17.0

  • new devel version for Bioc 3.2

MSnbase 1.15

Changes in version 1.15.18

  • fix failing test_MSnExp::readMSData unit test on Windows i386 (@.cache$size being different on that arch) [2015-04-14 Tue]
  • merge @vladpetyuk PR #50 fix of combine features bug [2015-04-14 Tue]

Changes in version 1.15.17

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

Changes in version 1.15.16

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

Changes in version 1.15.15

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

Changes in version 1.15.14

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

Changes in version 1.15.13

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

Changes in version 1.15.12

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

Changes in version 1.15.11

  • update malformed Description [2015-03-20 Fri]

Changes in version 1.15.10

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

Changes in version 1.15.9

  • use S4Vectors’ isEmpty generic [2015-03-10 Tue]

Changes in version 1.15.8

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

Changes in version 1.15.7

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

Changes in version 1.15.6

  • add intensity column to the calculateFragments output; closes #47;1 [2015-02-02 Mon]
  • add method argument to calculateFragments to allow the user choosing the highest/closest peak or all peaks in the tolerance range; closes #47;2 [2015-02-09 Mon]
  • add neutralLoss argument to calculateFragments and calculate loss of water and ammonia; closes #47:3 [2015-02-19 Thu]
  • new imputation methods via imputeLCMD and norm [2015-02-09 Mon]
  • vignette updates [2015-02-09 Mon]
  • imputation unit test [2015-02-24 Tue]

Changes in version 1.15.5

  • update dependency to mzID >= 1.5.2 [2015-01-28 Wed]
  • rewrite addIdentificationData and change its signature [2015-01-28 Wed]
  • add methods addIdentificationData which work on MSnExp and MSnSets using filenames (characters), mzID objects and data.frames; see #42; closes #45; [2015-01-28 Wed]
  • add a section about MSmaps in the vignette [2015-02-02 Mon]
  • MSmap has a new zeroIsNA argument to set all 0 values of the map to NA. This simplifies the resulting plot3D figure. [2015-02-02 Mon]

Changes in version 1.15.4

  • partly rewrite readMgfData [2015-01-19 Mon]
  • Typo in addIdentification data man [2015-01-20 Tue]
  • use Biocstyle [2015-01-23 Fri]
  • replace require with requireNamespace [2015-01-23 Fri]

Changes in version 1.15.3

  • plot,Spectrum2,character to add fragment ions based on peptide sequence [2014-11-20 Thu]
  • update vignette with above [2014-11-20 Thu]
  • comment parallel code in quantify man [2015-01-09 Fri]

Changes in version 1.15.2

  • merged sgibb’s pull request exporting overloaded methods as well [2014-11-02 Sun]
  • updated MSnSet validity, checking that exprs(.) is a matrix [2014-11-12 Wed]
  • fix error (missing header extraction) is MSmap example [2014-11-18 Tue]

Changes in version 1.15.1

  • Fixing error when id file has no spectrumFile info (see issue #39) and return a warning (instead of an error) when the file used to create the MSnExp/MSnSet and mzid file were different [2014-10-15 Wed]

Changes in version 1.15.0

  • Devel version for Bioc 3.1

MSnbase 1.14

Changes in version 1.14.0

  • Release version for Bioc 3.0

MSnbase 1.13

Changes in version 1.13.16

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

Changes in version 1.13.15

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

Changes in version 1.13.14

  • Fix xic example [2014-08-08 Fri]
  • importing lattice, ggplot2 (was depends) and suggesting rgl [2014-08-09 Sat]
  • MSmap infrastructure [2014-08-09 Sat]

Changes in version 1.13.13

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

Changes in version 1.13.12

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

Changes in version 1.13.11

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

Changes in version 1.13.10

  • new averageMSnSet function to generate an average over a list of MSnSets. [2014-06-17 Tue]
  • new non-parametric coefficent of variation function [2014-06-17 Tue]
  • Using/importing IRanges::width [2014-06-18 Wed]

Changes in version 1.13.9

  • new listOf helper function [2014-06-16 Mon]
  • compfnames to compare and document differences in MSnSet feature names [2014-06-16 Mon]
  • suggesting Vennerable (compfnames example) and roxygen2 (generate rd) [2014-06-16 Mon]

Changes in version 1.13.8

  • Add recommended biocView [2014-06-05 Thu]

Changes in version 1.13.7

  • Bug tracking link [2014-05-26 Mon]

Changes in version 1.13.6

  • new isEmpty method for Spectrum instances [2014-05-14 Wed]
  • removePeaks does not try for empty Spectra [2014-05-14 Wed]
  • isEmpty unit test [2014-05-14 Wed]

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

MSnbase 1.11

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

MSnbase 1.9

Changes in version 1.9.12

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

Changes in version 1.9.11

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

Changes in version 1.9.10

  • faster plotMzDelta [2013-09-28 Sat]
  • faster plotMzDelta for mzRramp instances [2013-09-29 Sun]
  • chromatogram method [2013-10-04 Fri]
  • plotMzDelta has subset arg [2013-10-04 Fri]
  • xic method [2013-10-04 Fri]
  • suggesting msdata for chromatogram example [2013-10-04 Fri]
  • renamed plotting arg ‘centroided.’ [2013-10-04 Fri]

Changes in version 1.9.9

  • typo in filterNA Rd [2013-09-18 Wed]
  • writeMgfData now has a progress bar [2013-09-24 Tue]
  • centroided(MSnExp) <- TRUE now allowed [2013-09-24 Tue]

Changes in version 1.9.8

  • using new.env(parent=emptyenv()) to get rid of enclosing env when creating new MSnExps [2013-09-17 Tue]
  • new (private) MSnExp.size function [2013-09-17 Tue]

Changes in version 1.9.7

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

Changes in version 1.9.6

  • new as.data.frame.MSnSet method [2013-08-16 Fri]
  • new ms2df function [2013-08-16 Fri]
  • new getEcols and grepEcols helpers for readMSnSet2 [2013-08-16 Fri]

Changes in version 1.9.5

  • 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

MSnbase 1.8

Changes in version 1.8.0

  • new Bioc 2.12 stable version

MSnbase 1.7

Changes in version 1.7.25

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

Changes in version 1.7.24

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

Changes in version 1.7.23

  • new private nologging function [2013-02-21 Thu]
  • adding total number of features on plotNA [2013-02-22 Fri]
  • updated msnbase.r [2013-02-26 Tue]

Changes in version 1.7.22

  • 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]

MSnbase 1.5

Changes in version 1.5.25

  • fixed bug when quantifying exp of length 1 (reported by Colin Archer), added test [2012-09-26 Wed]
  • fixed parallel default to FALSE [2012-09-26 Wed]

Changes in version 1.5.24

  • updated clean, removePeaks, combineFeatures, purityCorrect, trimMz, plot, MSnSet-class examples to not use readMSData [2012-09-25 Tue]
  • fixed clean,MSnExp-method [2012-09-25 Tue]
  • space in log message in extractPrecSpectra [2012-09-25 Tue]

Changes in version 1.5.23

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

Changes in version 1.5.22

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

Changes in version 1.5.21

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

Changes in version 1.5.20

  • an immediate warning is thrown is any(centroided(object)) in quantify.MSnExp [2012-09-15 Sat]
  • mzTab file and loading time is now recorded in processingData [2012-09-15 Sat]
  • temporarily dontrun’ing’ the mzTab read/write examples as -LS is down (and breaks rols) (note: modifed Rd files, not roxygen template) [2012-09-15 Sat]

Changes in version 1.5.19

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

Changes in version 1.5.18

  • new log method for MSnSet instances [2012-09-13 Thu]
  • new MAplot methods using generic and ma.plot/mva.pairs from affy [2012-09-13 Thu]

Changes in version 1.5.17

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

Changes in version 1.5.16

  • parallel quantify is now always set to FALSE on Windows, fixing example checking issues [2012-09-11 Tue]
  • fixed types in plotMzDelta man [2012-09-11 Tue]

Changes in version 1.5.15

  • 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

MSnbase 1.3

Changes in version 1.3.15

  • new updateFeatureNames function [2012-02-17 Fri]
  • updated vignettes to illustrate vertical/horizontal combine [2012-02-17 Fri]
  • typo in normalised.Rd [2012-02-19 Sun]
  • TODO combine unit tests

Changes in version 1.3.14

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

Changes in version 1.3.13

  • new plotNA method + doc [2012-02-15 Wed]
  • new filterNA method + doc + tests [2012-02-15 Wed]
  • added a check on ‘n’ in topN [2012-02-16 Thu]
  • created a .Rinstignore [2012-02-16 Thu]
  • Update package Rd [2012-02-16 Thu]

Changes in version 1.3.12

  • 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 [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

MSnbase 1.2

Changes in version 1.2.0

  • Version bump for Bioc 2.9 release

MSnbase 1.1

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 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]

MSnbase 0.99

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

  • 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

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.

MSnbase 0.1

Changes in version 0.1.5

  • added zoo to Suggest, as zoo::rollapply is used in vignette.
  • changes rollapply call to zoo:::rollapply.zoo, to make it work with zoo_1.6-4, rather that depending on zoo_1.7-0, which is not yet on CRAN (only r-forge).
  • added vns to Suggests, as it is used in the demo vignette.

Changes in version 0.1.4

  • 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

  • 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