Changes in version 2.1.18 ------------------------- - suggest reshape2, as it's used in vignette <2017-04-18 Tue> Changes in version 2.1.17 ------------------------- - Update NEWS file <2017-04-11 Tue> Changes in version 2.1.16 ------------------------- - Remove timing test as it fails occasionally on the Bioconductor servers <2017-04-09 Sun> Changes in version 2.1.15 ------------------------- - Remove reshape2 dependency; see #201 <2017-04-06 Thu> Changes in version 2.1.14 ------------------------- - Internal rewrite and speedup of topN; Briefly multiple apply calls are avoided, `getTopIdx` and `subsetById` are replaced by `.topIdx`. See PR #199 for details. <2017-03-20 Mon> - Fix mz calculation for terminal modifications and z > 1 in `calculateFragments`; closes #200 <2017-03-22 Wed> - Fix errors and notes <2017-03-30 Thu> Changes in version 2.1.13 ------------------------- - Internal rewrite and speedup of plotNA <2017-02-26 Sun> Changes in version 2.1.12 ------------------------- - Import dist from stats <2017-02-25 Sat> - Fix filing example <2017-02-25 Sat> Changes in version 2.1.11 ------------------------- - Fix breaks calculation for binning single (closes #191) and multiple (closes #190) spectra. The fix for single spectra (#191) could result in slightly different breaks on the upper end of the m/z values. <2017-02-10 Fri> - New `aggvar` function, to assess aggregation variability <2017-02-11 Sat> Changes in version 2.1.10 ------------------------- - New `diff.median` normalisation for `MSnSet`s. <2017-01-26 Thu> - Fix combineFeatures message <2017-02-01 Wed> Changes in version 2.1.9 ------------------------ - When fully trimmed, an (empty) spectrum has peaksCount of 0L - see https://github.com/lgatto/MSnbase/issues/184 <2017-01-20 Fri> - Add filterEmptySpectra,MSnExp method (see issue #181) <2017-01-20 Fri> - Add a section about notable on-disk and in-memory differences (was issue #165) <2017-01-20 Fri> Changes in version 2.1.8 ------------------------ - Remove order option altogether <2017-01-19 Thu> (superseeds setting default sorting using "auto" on R < 3.3 and "radix" otherwise <2017-01-03 Tue>) Changes in version 2.1.7 ------------------------ - Setting default sorting using "auto" on R < 3.3 and "radix" otherwise <2017-01-03 Tue> - filterMz returns an empty spectrum when no data is within the mz range (see issue #181) <2017-01-16 Mon> - Performance improvement: a new private .firstMsLevel will efficiently return the first MS level in an MSnExp and OnDiskMSnExp. See issue #183 for details/background <2017-01-18 Wed> Changes in version 2.1.6 ------------------------ - Migrate io and dev vignettes to BiocStyle's html_document2 style <2016-12-23 Fri> - Update show method to display class. - Migrated to NEWS.md <2016-12-23 Fri> - Update DESCRIPTION (and README) to reflect wider usage of MSnbase (replaced MS-based proteomics by mass spectrometry and proteomics) <2016-12-23 Fri> Changes in version 2.1.5 ------------------------ - Fix (unexported) navMS example code <2016-12-14 Wed> Changes in version 2.1.4 ------------------------ - Jo added netCDF support <2016-11-30 Wed> Changes in version 2.1.3 ------------------------ - FeaturesOfInterest collections can now be assigned names - addresses issue #172 <2016-11-25 Fri> Changes in version 2.1.2 ------------------------ - Update readMSnSet2 to save filename <2016-11-09 Wed> - Ensure that header information is read too if spectra data is loaded for onDiskMSnExp objects (see issue #170) <2016-11-24 Thu> Changes in version 2.1.1 ------------------------ - Fix typo in impute man page <2016-10-19 Wed> - Cite Lazar 2016 in vignette imputation section <2016-10-28 Fri> Changes in version 2.1.0 ------------------------ - New version for Bioconductor devel - New version for Bioconductor release version 3.4 Changes in version 1.99.6 ------------------------- - Reverting to old initialize,Spectrum (see issue #163) <2016-10-07 Fri> - Setting Spectrum class versions outside of prototype (see issue #163). For this, there is now a vector of class version in .MSnbaseEnv <2016-10-10 Mon> Changes in version 1.99.5 ------------------------- - Add removeReporters,OnDiskMSnExp (see issue #161 for details) <2016-10-07 Fri> Changes in version 1.99.4 ------------------------- - Fix bug in readMzTabData_v0.9 <2016-10-07 Fri> Changes in version 1.99.3 ------------------------- - Injection time is now added to the header when reading mzML files using readMSData2 (see issue #159) <2016-10-04 Tue> Changes in version 1.99.2 ------------------------- - Added isolationWindow,MSnExp method <2016-09-23 Fri> - Updated readMSData Spectrum2 class to support MS levels > 2 <2016-09-30 Fri> Changes in version 1.99.1 ------------------------- - Fix MS level test in quantify,OnDiskMSnExp to support MS2+ level quantitation <2016-09-14 Wed> Changes in version 1.99.0 ------------------------- - Add normalize method for onDiskMSnExp <2016-06-07 Tue>. - Fix bug in readMSData <2016-06-07 Tue>. - Added documentation and unit test for trimMz <2016-06-01 Wed>. - Added trimMz method for onDiskMSnExp objects <2016-05-31 Tue>. - Added (internal) method spectrapply to apply a function to all spectra of an onDiskMSnExp object; does the data import, subsetting, application of lazy processing steps etc. <2016-05-27 Fri>. - Added a section to the MSnbase-development vignette <2016-05-27 Fri>. - Finished with all pSet inherited methods and docs <2016-05-26 Thu>. - Added rtlim argument to spectra method for onDiskMSnExp <2016-05-26 Thu>. - Methods rtime, tic, ionCount, polarity and acquisitionNum implemented <2016-05-25 Wed>. - Documentation added for most methods <2016-05-25 Wed>. - Methods peaksCount and spectra for onDiskMSnExp objects implemented <2016-05-24 Tue>. - Performance and validation tests for the Spectrum1 C-constructor <2016-05-23 Mon>. - Spectrum1 constructor implemented in C (presently not exported) <2016-05-20> - length, scanIndex, acquisitionNum and centroided implemented <2016-05-20> - Implemented fromFile and msLevel for onDiskMSnExp <2016-05-19 Thu> - Implemented an onDiskMSnExp class for on-the-fly data import <2016-05-19 Thu> - Fixed the validate method for pSet to play nicely with onDiskMSnExp objects <2016-05-19 Thu> - Added slot onDisk to pSet objects (TRUE for onDiskMSnExp objects, FALSE otherwise). The getter method isOnDisk checks for the presence of the slot in the object (backward compatibility) <2016-05-19 Thu> - Implemented a ProcessingStep class that helps to keep track how (spectra) data should be processed on the fly <2016-05-18 Wed> - In onDiskMSnExp validity, check that the assaydata is empty <2016-06-28 Tue> - Pass neutralLoss in plot,Spectrum,Spectrum-method to .calculateFragments; fixes #146 <2016-08-12 Fri> - Allow the user to specify the `cex`, `lwd`, `pch` for peaks and fragments in plot,Spectrum,Spectrum-method; closes #148 <2016-08-12 Fri> - Update centroided with an na.fail argument (see issue #150 for details) <2016-08-12 Fri> - Fix warning in readMgfData if TITLE contains multiple "=" <2016-08-24 Wed> Changes in version 1.21.8 ------------------------- - Update MSnSet validity method to guard agains empty string feature names <2016-06-20 Mon> - Simplify show,MSnExp method to work for various MS level cases and onDiskMSnExp - addressed issue #98 <2016-06-28 Tue> - removeMultipleAssignment also removes features that were not assigned (i.e. that have fcol (nprots) NA) <2016-07-02 Sat> - New smoothed slot/accessor/replacement methods <2016-07-08 Fri> - Update reporter masses and add TMT10 ETD/HCD <2016-07-20 Wed> - returning empty spectrum when fliterMz has empty range - see issue #134 <2016-07-22 Fri> - (mz, intensity) values are reordered based on order(mz) - see issue #135 <2016-07-26 Tue> - fix bug in bin,Spectrum - see issue #137 <2016-08-05 Fri> Changes in version 1.21.7 ------------------------- - Update iPQF reference <2016-06-01 Wed> - Fix a bug in normalize method for MSnExp objects: assigning normalized spectra directly to assayData is not possible, as the environment is locked. See PR #91. - readMSData: if no phenodata is provided it creates an empty one with rownames corresponding to the file names. See PR #91. - Lock itraqdata's assaydata bindings <2016-06-08 Wed> Changes in version 1.21.6 ------------------------- - MSmap unit test <2016-05-23 Mon> - Fix bug in as(MSmap, "data.frame") <2016-05-23 Mon> Changes in version 1.21.5 ------------------------- - Added Johannes as contributor <2016-05-12 Thu> - Deprecate MzTab v0.9 <2016-05-19 Thu> - Fix old googlecode URLs to old MzTab <2016-05-19 Thu> Changes in version 1.21.4 ------------------------- - More MzTab and Spectrum1 unit testing <2016-05-08 Sun> - Speed up readMSData (PR #86 by jotsetung) <2016-05-12 Thu> - Replace example file URL to use github instead of googlecode <2016-05-12 Thu> Changes in version 1.21.3 ------------------------- - No fileNames replacement method <2016-05-07 Sat> - fileNames unit tests <2016-05-07 Sat> - add fileNames to class that had fileName accessor (MSmap, MzTab) <2016-05-07 Sat> Changes in version 1.21.2 ------------------------- - Check for rownames/fnames in readMSnSet2 and unit test <2016-05-05 Thu> Changes in version 1.21.1 ------------------------- - Fix wrong indexing in readMSdata, msLevel==1 (PR #85 by jotsetung) <2016-05-04 Wed> - grep/getEcols have a 'n' param specifying which line to grep/get <2016-05-04 Wed> Changes in version 1.21.0 ------------------------- - Version bump for new Bioc devel Changes in version 1.20.0 ------------------------- - Version bump for Bioc release version 3.3 Changes in version 1.19.24 -------------------------- - more unit tests and bug fixes <2016-04-30 Sat> <2016-05-02 Mon> Changes in version 1.19.23 -------------------------- - more unit tests and bug fixes <2016-04-27 Wed> <2016-04-28 Thu> Changes in version 1.19.22 -------------------------- - more unit tests <2016-04-23 Sat> <2016-04-24 Sun> <2016-04-26 Tue> - remove readIspyData functions <2016-04-23 Sat> - Fixed bug in error catching in utils.mergeSpectraAndIdentificationData <2016-04-23 Sat> Changes in version 1.19.21 -------------------------- - nadata.R unit tests and bugs fixed <2016-04-22 Fri> Changes in version 1.19.20 -------------------------- - Moved makeNaData[2] and whichNA (was in pRoloc) <2016-04-21 Thu> Changes in version 1.19.19 -------------------------- - new naplot function to visualise missing values as a heatmap and barplots along the samples and features. <2016-04-04 Mon> Changes in version 1.19.18 -------------------------- - fix typo in man <2016-04-02 Sat> Changes in version 1.19.17 -------------------------- - Write support of mzTab has been dropped (writeMzTabData, makeMTD, makePEP and makePRT are now defunct) <2016-03-18 Fri> Changes in version 1.19.16 -------------------------- - add estimateNoise,[Spectrum|MSnExp]-method; closes #78 <2016-03-10> - import a lot of functions from recommended packages, namely graphics, stats and utils to avoid many "Undefined global functions or variables" NOTEs in R CMD check <2016-03-10> Changes in version 1.19.15 -------------------------- - limit readMSData unit test due to Windows-only error <2016-03-09 Wed> - fix unit test for utils.colSd(x, na.rm=TRUE) Changes in version 1.19.14 -------------------------- - Document change in nQuants param fcol to groupBy <2016-03-02 Wed> Changes in version 1.19.13 -------------------------- - Fixed bug in bin_Spectrum, reported by Weibo Xie <2016-02-16 Tue> - Added unit test for bug above <2016-02-16 Tue> - Merged 'apply functions columnwise by group' <2016-02-16 Tue> - In nQuants, the fcol argument has been replaced with groupBy to make the signature consistent with featureCV <2016-02-16 Tue> Changes in version 1.19.12 -------------------------- - Moved polarity slot from Spectrum1 (0.1.0 -> 0.2.0) to Spectrum (0.2.0 -> 0.3.0) superclass; also bumped Spectrum2 class (0.1.0 -> 0.2.0) and MSnExp (0.3.0 -> 0.3.1, to trace changes in Spectrum2). Wrote MSnExp and Spectrum2 updateObject methods. <2016-02-11 Thu> Changes in version 1.19.11 -------------------------- - Fix trimws generic/methods with useAsDefault (see issue #75) <2016-02-02 Tue> - add exprs,MSnSet-method alias (since exprs is now exported) <2016-02-02 Tue> Changes in version 1.19.10 -------------------------- - export exprs, fvarLabels, and sampleNames[<-] <2016-01-30 Sat> Changes in version 1.19.9 ------------------------- - new trimws method for data.frames and MSnSets <2016-01-29 Fri> Changes in version 1.19.8 ------------------------- - readMSnSet2 now also accepts a data.frame as input <2016-01-29 Fri> - selective ggplot2 import <2016-01-29 Fri> Changes in version 1.19.7 ------------------------- - new sampleNames<- for pSet and MSnExp objects <2015-12-15 Tue> - Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat) <2015-12-18 Fri> Changes in version 1.19.6 ------------------------- - MSnExp feautreNames are now X01, X02 (0 after X) to maintain numerical sorting of ASCII characters; contributed by sgibb <2015-12-14 Mon> - Update MSnbase:::subsetBy to use split instead of lapply, which makes topN faster. This nevertheless changes the order of the resulting MSnSet (see issue #63 for details and background); contributed by sgibb <2015-12-14 Mon> Changes in version 1.19.5 ------------------------- - Merged pull request #67 from lgatto/featureCV by sgibb: featureCV ignores its na.rm argument <2015-12-12 Sat> Changes in version 1.19.4 ------------------------- - Replacement method for MSnSetList names <2015-11-24 Tue> Changes in version 1.19.3 ------------------------- - New argument fcol to selectFeatureData to select feature variables using a vector <2015-10-28 Wed> Changes in version 1.19.2 ------------------------- - new selectFeatureData function to subset the feature data <2015-10-24 Sat> Changes in version 1.19.1 ------------------------- - Remove generics that are defined in ProtGenerics <2015-10-15 Thu> Changes in version 1.19.0 ------------------------- - Bioc devel 3.3 Changes in version 1.18.0 ------------------------- - Bioc release 3.2 Changes in version 1.17.16 -------------------------- - new default parameter 'feature weight' in iPQF by Martina Fisher (see PR#65) <2015-10-07 Wed> Changes in version 1.17.15 -------------------------- - Fix typo in plot man <2015-08-23 Sun> Changes in version 1.17.14 -------------------------- - Fix typo in impute man <2015-08-17 Mon> Changes in version 1.17.13 -------------------------- - partly rewrite writeMgfData <2015-05-16 Thu> - initial hmap function <2015-07-16 Thu> - fix bug in plotting MS1 spectra (closes issue #59) <2015-07-16 Thu> - new image implementation, based on @vladpetyuk's vp.misc::image_msnset <2015-07-25 Sat> - Changed the deprecated warning to a message when reading MzTab data version 0.9, as using the old reader can not only be achived by accident and will be kept for backwards file format compatibility <2015-07-30 Thu> Changes in version 1.17.12 -------------------------- - fix show MIAPE when some otherInfo at NA <2015-07-15 Wed> Changes in version 1.17.11 -------------------------- - adding unit tests <2015-07-01 Wed> - fix abundance column selection when creating MSnSet form MzTab <2015-07-01 Wed> - new mzTabMode and mzTabType shortcut accessors for mode and type of an mzTab data <2015-07-01 Wed> Changes in version 1.17.10 -------------------------- - Fix URL <2015-06-30 Tue> Changes in version 1.17.9 ------------------------- - calculateFragments' "neutralLoss" argument is now a list (was a logical before), see #47. <2015-06-24 Wed> - add defaultNeutralLoss() function to fill calculateFragments' modified "neutralLoss" argument, see #47. <2015-06-24 Wed> Changes in version 1.17.8 ------------------------- - coercion from IBSpectra to MSnSet, as per user request <2015-06-23 Tue> - new iPQF combineFeature method <2015-06-24 Wed> Changes in version 1.17.7 ------------------------- - Fix support of identification-only mzTab files <2015-06-22 Mon> Changes in version 1.17.6 ------------------------- - Export metadata,MzTab-method <2015-06-19 Fri> - Replace spectra,MzTab-method by psms,MzTab-method <2015-06-20 Sat> - Change the meaning of calculateFragments' "modifications" argument. Now the modification is added to the mass of the amino acid/peptide. Before it was replaced. <2015-06-21 Sun> - calculateFragments gains the feature to handle N-/C-terminal modifications, see #47. <2015-06-21 Sun> - update readMzTabData example <2015-06-22 Mon> Changes in version 1.17.5 ------------------------- - new MzTab class to store a simple parsing of an mzTab version 1 data file. See ?MzTab for details. <2015-06-16 Tue> Changes in version 1.17.4 ------------------------- - New lengths method for FoICollection instances <2015-06-06 Sat> - New image2 function for matrix object, that behaves like the method for MSnSets <2015-06-10 Wed> - image,MSnSet labels x and y axis as Samples and Features <2015-06-10 Wed> - fixed bug in purityCorrect, reported by Dario Strbenac <2015-06-11 Thu> Changes in version 1.17.3 ------------------------- - iTRAQ 8-plex correction factors and impurity matrix <2015-05-22 Fri> Changes in version 1.17.2 ------------------------- - new filterZero function <2015-05-01 Fri> Changes in version 1.17.1 ------------------------- - new MSnSetList class <2015-04-19 Sun> - new commonFeatureNames function <2015-04-14 Tue> - new compareMSnSets function <2015-04-19 Sun> - splitting and unsplitting MSnSets/MSnSetLists <2015-04-19 Sun> Changes in version 1.17.0 ------------------------- - new devel version for Bioc 3.2 Changes in version 1.15.18 -------------------------- - fix failing test_MSnExp::readMSData unit test on Windows i386 (@.cache$size being different on that arch) [2015-04-14 Tue] - merge @vladpetyuk PR #50 fix of combine features bug [2015-04-14 Tue] Changes in version 1.15.17 -------------------------- - add TMT10 paragraph and fig to demo vignette [2015-04-09 Thu] Changes in version 1.15.16 -------------------------- - support for TMT10 plex [2015-04-08 Wed] Changes in version 1.15.15 -------------------------- - using serial parallelisation during quantitation in unit tests [2015-04-02 Thu] Changes in version 1.15.14 -------------------------- - new msnset data, used in various examples instead of quantifying the itraqdata experiment over and over again [2015-04-01 Wed] Changes in version 1.15.13 -------------------------- - improve nbavg imputation description and add example [2015-03-22 Sun] - reduce compareSpectra example timing [2015-03-30 Mon] Changes in version 1.15.12 -------------------------- - average neighbour imputation for ordered fractions along a gradient [2015-03-21 Sat] Changes in version 1.15.11 -------------------------- - update malformed Description [2015-03-20 Fri] Changes in version 1.15.10 -------------------------- - update compareSpectra man [2015-03-19 Thu] - ExpressionSet <-> MSnSet coercion [2015-03-19 Thu] Changes in version 1.15.9 ------------------------- - use S4Vectors' isEmpty generic [2015-03-10 Tue] Changes in version 1.15.8 ------------------------- - Improved imputation section in demo vignette [2015-03-05 Thu] Changes in version 1.15.7 ------------------------- - Importing ProtGenerics [2015-02-28 Sat] - selective import of MALDIquant [2015-03-02 Mon] Changes in version 1.15.6 ------------------------- - add intensity column to the calculateFragments output; closes #47;1 [2015-02-02 Mon] - add method argument to calculateFragments to allow the user choosing the highest/closest peak or all peaks in the tolerance range; closes #47;2 [2015-02-09 Mon] - add neutralLoss argument to calculateFragments and calculate loss of water and ammonia; closes #47:3 [2015-02-19 Thu] - new imputation methods via imputeLCMD and norm [2015-02-09 Mon] - vignette updates [2015-02-09 Mon] - imputation unit test [2015-02-24 Tue] Changes in version 1.15.5 ------------------------- - update dependency to mzID >= 1.5.2 [2015-01-28 Wed] - rewrite addIdentificationData and change its signature [2015-01-28 Wed] - add methods addIdentificationData which work on MSnExp and MSnSets using filenames (characters), mzID objects and data.frames; see #42; closes #45; [2015-01-28 Wed] - add a section about MSmaps in the vignette [2015-02-02 Mon] - MSmap has a new zeroIsNA argument to set all 0 values of the map to NA. This simplifies the resulting plot3D figure. [2015-02-02 Mon] Changes in version 1.15.4 ------------------------- - partly rewrite readMgfData [2015-01-19 Mon] - Typo in addIdentification data man [2015-01-20 Tue] - use Biocstyle [2015-01-23 Fri] - replace require with requireNamespace [2015-01-23 Fri] Changes in version 1.15.3 ------------------------- - plot,Spectrum2,character to add fragment ions based on peptide sequence [2014-11-20 Thu] - update vignette with above [2014-11-20 Thu] - comment parallel code in quantify man [2015-01-09 Fri] Changes in version 1.15.2 ------------------------- - merged sgibb's pull request exporting overloaded methods as well [2014-11-02 Sun] - updated MSnSet validity, checking that exprs(.) is a matrix [2014-11-12 Wed] - fix error (missing header extraction) is MSmap example [2014-11-18 Tue] Changes in version 1.15.1 ------------------------- - Fixing error when id file has no spectrumFile info (see issue #39) and return a warning (instead of an error) when the file used to create the MSnExp/MSnSet and mzid file were different [2014-10-15 Wed] Changes in version 1.15.0 ------------------------- - Devel version for Bioc 3.1 Changes in version 1.14.0 ------------------------- - Release version for Bioc 3.0 Changes in version 1.13.16 -------------------------- - width generic if non-existant [2014-09-03 Wed] - fix undocumented S4 methods warnings [2014-09-27 Sat] Changes in version 1.13.15 -------------------------- - msMap(MSmap)<- method [2014-08-12 Tue] - Typo in MIAPE man [2014-08-29 Fri] Changes in version 1.13.14 -------------------------- - Fix xic example [2014-08-08 Fri] - importing lattice, ggplot2 (was depends) and suggesting rgl [2014-08-09 Sat] - MSmap infrastructure [2014-08-09 Sat] Changes in version 1.13.13 -------------------------- - fix issue with readMSnSet2 without fdata [2014-07-28 Mon] Changes in version 1.13.12 -------------------------- - Don't import width from IRanges [2014-07-23 Wed] - qual slot is populated again [2014-07-23 Wed] Changes in version 1.13.11 -------------------------- - remove Vennerable::Venn from example and DESCRIPTION [2014-06-19 Thu] Changes in version 1.13.10 -------------------------- - new averageMSnSet function to generate an average over a list of MSnSets. [2014-06-17 Tue] - new non-parametric coefficent of variation function [2014-06-17 Tue] - Using/importing IRanges::width [2014-06-18 Wed] Changes in version 1.13.9 ------------------------- - new listOf helper function [2014-06-16 Mon] - compfnames to compare and document differences in MSnSet feature names [2014-06-16 Mon] - suggesting Vennerable (compfnames example) and roxygen2 (generate rd) [2014-06-16 Mon] Changes in version 1.13.8 ------------------------- - Add recommended biocView [2014-06-05 Thu] Changes in version 1.13.7 ------------------------- - Bug tracking link [2014-05-26 Mon] Changes in version 1.13.6 ------------------------- - new isEmpty method for Spectrum instances [2014-05-14 Wed] - removePeaks does not try for empty Spectra [2014-05-14 Wed] - isEmpty unit test [2014-05-14 Wed] Changes in version 1.13.5 ------------------------- - export .get.amino.acids function [2014-05-08 Thu] - removePeaks for centroided data [2014-05-08 Thu] - add new exported function get.atomic.mass [2014-05-08 Thu] - Spectrum[2] prototype sets centroided=FALSE by default (instead of logical()) [2014-05-08 Thu] - fnamesIn also supports y = "data.frame" [2014-05-14 Wed] - Using BiocParallel for parallel support; replaced parallel argument with BPPARAM [2014-05-14 Wed] Changes in version 1.13.4 ------------------------- - Document difference between traceable and non-traceable FeaturesOfInterest instances [2014-04-30 Wed] - ignoring desciptions with length > 1 [2014-04-30 Wed] Changes in version 1.13.3 ------------------------- - FeaturesOfInterest [2014-04-29 Tue] Changes in version 1.13.2 ------------------------- - add compareSpectra to compare Spectrum objects [2014-04-09 Wed] - add bin method for Spectrum objects [2014-04-09 Wed] - recreate inst/extdata/msx.rda for R 3.1 and Biobase 2.24 [2014-04-13 Sun] - add plot,Spectrum,Spectrum method [2014-04-14 Mon] - add calculateFragments,character,Spectrum and calculateFragments,character,missing methods [2014-04-15 Tue] - updated readMSData test unit to ignore object@.__classVersion__ that fails with latest R/Bioc versions [2014-04-15 Tue] - formatRt conversion from 'mm:sec' to sec and unit test [2014-04-17 Thu] - Update nprot/npsm.prot/npsm.pep/npep.prot feature variables and relevant man/tests/argument defaults [2014-04-17 Thu] Changes in version 1.13.1 ------------------------- - add precursor method to Spectrum2 normalisation method [2014-04-08 Tue] - add smooth for MSnExp and Spectrum classes [2014-04-10 Thu] - add pickPeaks for MSnExp and Spectrum classes [2014-04-10 Thu] - updated show,MSnExp to display only first/last files when > 2 [2014-04-11 Fri] Changes in version 1.13.0 ------------------------- - New devel version for Bioc 3.0 Changes in version 1.11.14 -------------------------- - update dependency to R >= 3.1 [2014-04-05 Sat] Changes in version 1.11.13 -------------------------- - Document [get|grep]Ecols in io vignette [2014-03-31 Mon] - typo in readMSnSet man [2014-03-31 Mon] - updated affiliation in vignettes [2014-03-31 Mon] Changes in version 1.11.12 -------------------------- - Fixed a bug in readMzTabData reported by Hendrik Weisser [2014-03-26 Wed] Changes in version 1.11.11 -------------------------- - precomputed msx test data now has id data [2014-03-25 Tue] - quantitation unit tests [2014-03-25 Tue] - quantify method now accepts label-free methods [2014-03-25 Tue] Changes in version 1.11.10 -------------------------- - import mzID [2014-03-20 Thu] - dummyiTRAQ id extdata [2014-03-21 Fri] - add addIdentificationData method for MSnExp and MSnSet [2014-03-21 Fri] - using data from pRolocdata (was pRoloc) [2014-03-23 Sun] - added removeNoId,MSnExp,MSnSet methods [2014-03-23 Sun] - added idSummary,MSnExp,MSnSet methods [2014-03-24 Mon] - Not generating different sample per file when reading raw data. pData(.) now has systematically 1 row if not specifically provided by the user. A message is also reported by validity,pSet if row(pData(.)) > 1. [2014-03-24 Mon] - NAnnotatedDataFrame now has default multiplex 1 [2014-03-25 Tue] - NAnnotatedDataFrame unit tests [2014-03-25 Tue] Changes in version 1.11.9 ------------------------- - write.exprs can have fDataCol or fcol (for consistence) [2014-03-17 Mon] - Fixing bug in combineFeatures(..., is.character(groupBy)) [2014-03-19 Wed] - fixed combineFeatures [2014-03-20 Thu] - added example, test and doc for combineFeatures with list [2014-03-20 Thu] Changes in version 1.11.8 ------------------------- - adding redundancy handling to combineFeatures (by vladpetyuk, pull request #18) [2014-03-14 Fri] - updated combineFeatures signature to accomodate above changes [2014-03-14 Fri] - updated unit tests for new testhat 0.8 [2014-03-14 Fri] Changes in version 1.11.7 ------------------------- - NA Changes in version 1.11.6 ------------------------- - add corresponding xcms functions to the chromatogram and xic manual page [2014-02-21 Fri] - new bpca imputation methods [2014-02-27 Thu] - replacing stop_on_error with option in vignette [2014-02-27 Thu] Changes in version 1.11.5 ------------------------- - typo in MSnSet droplevels man [2014-01-27 Mon] - typo in MSnbase-demo vignette [2014-02-20 Thu] - fix BPI legend in chromatogram [2014-02-20 Thu] Changes in version 1.11.4 ------------------------- - passing ... to sweep when normalising [2013-12-08 Sun] - updated makeMTD to accomodate new MS ontology [2013-12-23 Mon] Changes in version 1.11.3 ------------------------- - updated mzTab example files to new url [2013-11-15 Fri] - warning about mzTab versions [2013-11-15 Fri] Changes in version 1.11.2 ------------------------- - move inst/doc to vignettes [2013-10-19 Sat] Changes in version 1.11.1 ------------------------- - document na.rm in combineFeatures Rd [2013-10-18 Fri] Changes in version 1.11.0 ------------------------- - New devel version for Bioc 2.14 Changes in version 1.9.12 ------------------------- - fix MSnSet -] ExpressionSet [2013-10-13 Sun] - MSnSet -] ExpressionSet unit test [2013-10-13 Sun] Changes in version 1.9.11 ------------------------- - MIAPE to MIAME conversion [2013-10-11 Fri] - proper MIAME when MSnSet -] ExpressionSet [2013-10-11 Fri] Changes in version 1.9.10 ------------------------- - faster plotMzDelta [2013-09-28 Sat] - faster plotMzDelta for mzRramp instances [2013-09-29 Sun] - chromatogram method [2013-10-04 Fri] - plotMzDelta has subset arg [2013-10-04 Fri] - xic method [2013-10-04 Fri] - suggesting msdata for chromatogram example [2013-10-04 Fri] - renamed plotting arg 'centroided.' [2013-10-04 Fri] Changes in version 1.9.9 ------------------------ - typo in filterNA Rd [2013-09-18 Wed] - writeMgfData now has a progress bar [2013-09-24 Tue] - centroided(MSnExp) <- TRUE now allowed [2013-09-24 Tue] Changes in version 1.9.8 ------------------------ - using new.env(parent=emptyenv()) to get rid of enclosing env when creating new MSnExps [2013-09-17 Tue] - new (private) MSnExp.size function [2013-09-17 Tue] Changes in version 1.9.7 ------------------------ - Passing ... to read.table in MSnbase:::readIspy[Silac|15N]Data [2013-09-16 Mon] - QualityControl biocView [2013-09-16 Mon] Changes in version 1.9.6 ------------------------ - new as.data.frame.MSnSet method [2013-08-16 Fri] - new ms2df function [2013-08-16 Fri] - new getEcols and grepEcols helpers for readMSnSet2 [2013-08-16 Fri] Changes in version 1.9.5 ------------------------ - typo in Author[s]@R [2013-05-15 Wed] Changes in version 1.9.4 ------------------------ - new simple MSnSet constructor [2013-05-07 Tue] Changes in version 1.9.3 ------------------------ - Using knitr as VignetteEngine [2013-04-29 Mon] - Remove LazyLoad from DESCRIPTION, which is default nowadays [2013-04-29 Mon] - knitr dependency ] 1.1.0 for VignetteBuilder [2013-04-29 Mon] - Adding MSnSet creating sections in io vignette [2013-04-29 Mon] - new readMSnSet2 function [2013-04-30 Tue] Changes in version 1.9.2 ------------------------ - clean has now a all param (default FALSE is retain original behavious) to remove all 0 intensity values [2013-04-17 Wed] - using BiocGenerics::normalize [2013-04-25 Thu] Changes in version 1.9.1 ------------------------ - new logging utility function to update an MSnSet's processingData(object)$processing [2013-03-29 Fri] - Proper logging in t.MSnSet [2013-03-29 Fri] Changes in version 1.9.0 ------------------------ - new Bioc 2.13 devel version Changes in version 1.8.0 ------------------------ - new Bioc 2.12 stable version Changes in version 1.7.25 ------------------------- - updated itraqdata to fix issue in vignette when combine(exp1, exp2) and different MIAPE versions [2013-03-22 Fri] Changes in version 1.7.24 ------------------------- - Mention scale in vignette [2013-03-02 Sat] - exprsToRatio matrix method [2013-03-20 Wed] Changes in version 1.7.23 ------------------------- - new private nologging function [2013-02-21 Thu] - adding total number of features on plotNA [2013-02-22 Fri] - updated msnbase.r [2013-02-26 Tue] Changes in version 1.7.22 ------------------------- - msnbase.r na.rm arg [2013-02-20 Wed] Changes in version 1.7.21 ------------------------- - Added impute method [2013-02-19 Tue] Changes in version 1.7.20 ------------------------- - Explicitating that normalise and normalize are the same methods in the man. [2013-02-13 Wed] Changes in version 1.7.19 ------------------------- - adding MIAPE and pSet accessors: analyserDetails, analyzerDetails, ionSourceDetails, instrumentModel, instrumentManufacturer, instrumentCustomisations [2013-02-12 Tue] - switching back to analyserDetails slot [2013-02-12 Tue] Changes in version 1.7.18 ------------------------- - readMgfData now supports comments and PEPMASS with precursor mz and intensity, requested by Thomas Taus [2013-02-11 Mon] - improved and running read/writeMgfData example [2013-02-11 Mon] - new scanIndex accessor method [2013-02-11 Mon] Changes in version 1.7.17 ------------------------- - added a analyzer accessors/slot to accomodate new mzTab files with more meta-data [2013-01-30 Wed] Changes in version 1.7.16 ------------------------- - fixing knitr 1.0 compatibility [2013-01-15 Tue] Changes in version 1.7.15 ------------------------- - new scale method [2013-01-11 Fri] - renaming scale.mean and scale.median normalisation methods to center.mean and centre.median [2013-01-11 Fri] Changes in version 1.7.14 ------------------------- - new unexported readIspy15NData [2013-01-09 Wed] - min.int readIspy[Silac|15N]Data arg [2013-01-11 Fri] Changes in version 1.7.13 ------------------------- - msnbase.r v0.1.1 with oh (help) arg [2013-01-08 Tue] - msnbase.r coerce ob arg to numeric [2013-01-08 Tue] - testing if any features left in readIspyData [2013-01-08 Tue] Changes in version 1.7.12 ------------------------- - updated makeImpuritiesMatrix to create matrix from csv file with correction factors [2012-12-23 Sun] - makeImpuritiesMatrix test [2012-12-23 Sun] - readIspyData: message instead of warning if NA in featureData [2012-12-24 Mon] - Added msnbase.r script [2012-12-24 Mon] Changes in version 1.7.11 ------------------------- - new 'pattern' argument to filterNA [2012-12-15 Sat] - vignette and man updates [2012-12-15 Sat] - filterNA(, pattern) tests [2012-12-15 Sat] Changes in version 1.7.10 ------------------------- - new droplevels.MSnSet S3 method [2012-12-14 Fri] - fixed errors in vignette and udpates [2012-12-14 Fri] - vignette build stops in case of error [2012-12-14 Fri] Changes in version 1.7.9 ------------------------ - Updating processing data on readIspyData [2012-12-05 Wed] - filterNA has a droplevels arg [2012-12-05 Wed] - featureCV's default cv.norm is 'sum' now [2012-12-11 Tue] - fixed featureCV for 1 sample [2012-12-11 Tue] Changes in version 1.7.8 ------------------------ - new featureCV function [2012-12-04 Tue] - more MSnSet combineFeatures tests [2012-12-04 Tue] - new TMT6 impurity matrix and fixed purityCorrect [2012-12-05 Wed] - combineFeatures now automatically computes feature CVs (using featureCV) and collates this in featureData [2012-12-05 Wed] - new exprsToRatios method (moved from pRoloc) [2012-12-05 Wed] - initial implementation of impurity correction using Cramer's rule (see MSnbase:::cramer4) [2012-12-05 Wed] Changes in version 1.7.7 ------------------------ - added scale.mean and scale.median MSnSet normalisation method [2012-11-30 Fri] - improvements to readMSData [2012-11-30 Fri] - small updates to caching code, max level 2 [2012-11-30 Fri] - readMSdata test [2012-12-01 Sat] Changes in version 1.7.6 ------------------------ - Fixed bug in readIspyData, reported by Claire Mulvey [2012-11-27 Tue] Changes in version 1.7.5 ------------------------ - dropping levels in readIspySilacData [2012-11-06 Tue] - fixed plotNA [2012-11-09 Fri] Changes in version 1.7.4 ------------------------ - exporting log method [2012-11-02 Fri] - private readIspySilacData function [2012-11-05 Mon] - updating '['-MSnSet to log intial/final dims [2012-11-05 Mon] Changes in version 1.7.3 ------------------------ - updating readMzTabData to properly capture experiment description [2012-10-12 Fri] Changes in version 1.7.2 ------------------------ - fixed readMSData for MS1 [2012-10-08 Mon] Changes in version 1.7.1 ------------------------ - fixed vignettes [2012-10-02 Tue] Changes in version 1.7.0 ------------------------ - Version bump for next devel release [2012-10-01 Mon] Changes in version 1.5.25 ------------------------- - fixed bug when quantifying exp of length 1 (reported by Colin Archer), added test [2012-09-26 Wed] - fixed parallel default to FALSE [2012-09-26 Wed] Changes in version 1.5.24 ------------------------- - updated clean, removePeaks, combineFeatures, purityCorrect, trimMz, plot, MSnSet-class examples to not use readMSData [2012-09-25 Tue] - fixed clean,MSnExp-method [2012-09-25 Tue] - space in log message in extractPrecSpectra [2012-09-25 Tue] Changes in version 1.5.23 ------------------------- - updated quantify documentation [2012-09-24 Mon] - changed all foo.class functions to foo_class [2012-09-24 Mon] Changes in version 1.5.22 ------------------------- - setting parallel default to FALSE [2012-09-22 Sat] - enhanced parallel in DESCRIPTION and detectCores() passed to registerDoMC [2012-09-23 Sun] Changes in version 1.5.21 ------------------------- - removed registerDoMC no visible global function NOTE [2012-09-21 Fri] - fixed NOTE about xvarname which was a bug [2012-09-21 Fri] Changes in version 1.5.20 ------------------------- - an immediate warning is thrown is any(centroided(object)) in quantify.MSnExp [2012-09-15 Sat] - mzTab file and loading time is now recorded in processingData [2012-09-15 Sat] - temporarily dontrun'ing' the mzTab read/write examples as -LS is down (and breaks rols) (note: modifed Rd files, not roxygen template) [2012-09-15 Sat] Changes in version 1.5.19 ------------------------- - updated all ReporterIons rda data [2012-09-13 Thu] - Using && in testing parallel, require(foreach and doMC) [2012-09-14 Fri] Changes in version 1.5.18 ------------------------- - new log method for MSnSet instances [2012-09-13 Thu] - new MAplot methods using generic and ma.plot/mva.pairs from affy [2012-09-13 Thu] Changes in version 1.5.17 ------------------------- - changed TMT7[7] mass from 229.26 to 230.17 and ReporterIons descriptions [2012-09-12 Wed] Changes in version 1.5.16 ------------------------- - parallel quantify is now always set to FALSE on Windows, fixing example checking issues [2012-09-11 Tue] - fixed types in plotMzDelta man [2012-09-11 Tue] Changes in version 1.5.15 ------------------------- - updating code to ggplot2 v0.9.2 [2012-09-07 Fri] Changes in version 1.5.14 ------------------------- - added platform test to use doMC (d.tenenbaum) [2012-08-31 Fri] Changes in version 1.5.13 ------------------------- - updated fillUp function [2012-08-15 Wed] - added tikzDevice to suggests [2012-08-16 Thu] - tikzDevice no longer on CRAN - removing from Suggests and using pdf as device in vignette [2012-08-16 Thu] Changes in version 1.5.12 ------------------------- - using knitr instead of pgfSweave and misc vignette updated[2012-08-13 Mon] - spectrum2 reporter plotting params updates [2012-08-14 Tue] - added reporterNames to NAMESPACE [2012-08-14 Tue] Changes in version 1.5.11 ------------------------- - type in filterNA log messaging and also rounding pNA [2012-06-07 Thu] - typo in demo vignette - Gb instead of Mb [2012-07-15 Sun] Changes in version 1.5.10 ------------------------- - Fixed readMSData instrumentInfo handling (reported by Gopuraja Dharmalingam) [2012-06-05 Tue] - new multiple file loading test in test_io [2012-06-05 Tue] Changes in version 1.5.9 ------------------------ - topN now properly updates processingData [2012-06-01 Fri] - combineFeatures updates featureNames based on the groupBy argument - updated demo vignette and man accordinlgy [2012-06-01 Fri] - additional parameters were not passed when normalise using vsn [2012-06-01 Fri] Changes in version 1.5.8 ------------------------ - added aa data in environment data.frame [2012-05-22 Tue] - fixed MSnbase:::subsetBy (used by topN) when ncol(object) == 1 [2012-05-25 Fri] - new nQuants function [2012-05-31 Thu] - minor vignettes updates [2012-05-31 Thu] - nQuants now return a matrix with col names, taken form sampleNames(object) [2012-05-31 Thu] Changes in version 1.5.7 ------------------------ - changed title method to exptitle to avoid conflict/confusion with graphics::title and consitency with expinfo method [2012-05-15 Tue] - changed email to expemail [2012-05-15 Tue] - Added rols to Suggests [2012-05-15 Tue] Changes in version 1.5.6 ------------------------ - new ionSource, analyser, detectorType, title accessor methods for MIAPE, pSet and MSnSet classes [2012-05-06 Sun] - updated quantify example to use data(itraqdata) instead of reading dummyiTRAQ.mzXML [2012-05-09 Wed] - initial mzTab write support [2012-05-10 Thu] - mzTab read support [2012-05-10 Thu] - updated demo and io vignettes with mzTab info [2012-05-10 Thu] Changes in version 1.5.5 ------------------------ - added email slot in MIAPE and accessor [2012-05-04 Fri] - added expinfo methods to pSet and MSnSet [2012-05-04 Fri] - updated itraqdata [2012-05-04 Fri] - misc man typos fixed [2012-05-04 Fri] - quantify now properly propagates processingData [2012-05-04 Fri] Changes in version 1.5.4 ------------------------ - automatically populating experiment data instrument info while reading data [2012-04-30 Mon] - msInfo fixed and exported [2012-04-30 Mon] - update demo vignette with 14 fractions analysis paragraph [2012-05-01 Tue] Changes in version 1.5.3 ------------------------ - extractSpectra is now defunct [2012-04-20 Fri] - caching full header in level 1; this is required when and MSnExp instance with *many* spectra (created from many raw files) is quantified - calling header(object) is a too big overhead compared to actual reporter quantification. [2012-04-20 Fri] - The header() method now uses the cached dataframe if level ]= 1; the (unexported) .header function can be used to generate the dataframe using the assayData slot data. [2012-04-20 Fri] - Setting processingData in MSnSet initialisation. [2012-04-20 Fri] - Dropping index column from header. [2012-04-20 Fri] - new Spectrum class v0.2.0 has tic slot. [2012-04-21 Sat] - *tic* method (data stored as a Spectrum slot) now returns _total ion current_ (as commonly used) and _total ion count_ is obtain using *ionCount*. [2012-04-21 Sat] - fixed normalisation boxplot titles and other tic/ionCount changes in demo vignette. [2012-04-21 Sat] - removed qual subetting in MSnSet's "[" method [2012-04-24 Tue] Changes in version 1.5.2 ------------------------ - transposing and MSnSet does _silently_ drop the protocolData now [2012-04-03 Tue] - fixed MSnExp pData creation for multiple files, feature names have a .fileNumber extension now. [2012-04-19 Thu] - testing for uniqueness of files (filenames) in readMSData [2012-04-19 Thu] - updated itraqdata.RData [2012-04-19 Thu] - added a paralle argument to quantify and using paralle = FALSE in vignette, to avoid duplicated display of the command [2012-04-19 Thu] - defined "reporterNames<-" generics [2012-04-19 Thu] - fixed warning in readMSData where all not used for comparison of verctors of length ] 1 [2012-04-20 Fri] Changes in version 1.5.1 ------------------------ - updated NA warning message in readIspyData [2012-03-05 Mon] - fixed combineFeatures/combineMatrixFeatures for 1 sample [2012-03-20 Tue] - image method for MSnSet instances [2012-03-20 Tue] - fixed bug in plotNA (first t was wring) [2012-03-21 Wed] - import plot from stats4 [2012-03-21 Wed] - using reshape2 [2012-03-30 Fri] Changes in version 1.5.0 ------------------------ - new devel version bump Changes in version 1.3.15 ------------------------- - new updateFeatureNames function [2012-02-17 Fri] - updated vignettes to illustrate vertical/horizontal combine [2012-02-17 Fri] - typo in normalised.Rd [2012-02-19 Sun] - TODO combine unit tests Changes in version 1.3.14 ------------------------- - new is.na.MSnSet [2012-02-16 Thu] - updated vignette and NA related man pages with cross-links [2012-02-16 Thu] Changes in version 1.3.13 ------------------------- - new plotNA method + doc [2012-02-15 Wed] - new filterNA method + doc + tests [2012-02-15 Wed] - added a check on 'n' in topN [2012-02-16 Thu] - created a .Rinstignore [2012-02-16 Thu] - Update package Rd [2012-02-16 Thu] Changes in version 1.3.12 ------------------------- - new topN methods + doc + tests [2012-02-14 Tue] Changes in version 1.3.11 ------------------------- - changed explicit close(file) in writeMgf methods to on.exit(close(file)) [2012-02-12 Sun] - typo in vignette [2012-02-13 Mon] Changes in version 1.3.10 ------------------------- - type in writeMgfData man [2012-02-07 Tue] - updated TITLE in writeMgfData [2012-02-08 Wed] Changes in version 1.3.9 ------------------------ - updated demo vignette [2012-02-03 Fri] - sorting numeric subsets in "[" pSet, as unsorted numerical indexes fails [2012-02-03 Fri] - Added match.arg in combineFeatures so that a unique default value (the first) is used when no fun is specified [2012-02-03 Fri] Changes in version 1.3.8 ------------------------ - Modified trimMz warning to report acquisition number [2012-02-01 Wed] - add 'experimentData(object, value) <- ' method for signature eSet and MIAPE [2012-02-02 Thu] - combine methods for MIAPE instances [2012-02-02 Thu] - combine methods for MSnProcess instances [2012-02-02 Thu] - changed qual drop warning into message in combineFeatures, updated test_MSnSet accordingly [2012-02-02 Thu] - new updateFvarLabels and updateSampleNames function [2012-02-03 Fri] - combine method for MSnSets [2012-02-03 Fri] - Updated demo vignette figure 8 [2012-02-03 Fri] Changes in version 1.3.7 ------------------------ - Speeded up writeMgfData [2012-01-28 Sat] - fixes for ggplot2 0.9.0 - added import(grid) and import(reshape) [2012-01-30 Mon] - importFrom(plyr, ...) instead of only llply [2012-01-31 Tue] - loading reshape and grid in vignette [2012-01-31 Tue] - fixed chunk 21 (label = quantitation-plot) [2012-01-31 Tue] Changes in version 1.3.6 ------------------------ - Updated NoteAboutSpeedAndMemory since parallel processing has been added. [2011-12-18 Sun] - Added CITATION [2012-01-27 Fri] - Added information to header output: acquisition number and precursor intensity [2012-01-27 Fri] - Added a test in plot.Spectrum2 for empty dataframe [2012-01-27 Fri] - moved foreach, doMC to enhances [2012-01-27 Fri] Changes in version 1.3.5 ------------------------ - added a gc() before mzR::close(msdata)... seems to help with Rcpp and ref classes issue. [2011-12-09 Fri] - added a show parameter to getCacheEnv to define .cache should be printed out before being returned. [2011-12-09 Fri] - added cache unit test [2011-12-09 Fri] - readMzXMLData is now defunct and remove xcms from Imports [2011-12-16 Fri] Changes in version 1.3.4 ------------------------ - fixed bug in show MSnExp method for MS1 experiments. When loading MS1 spectra, cache is set to 0. Bug reported by Jesse Meyer. [2011-12-06 Tue] - fixed another bug/typo in readMSData [2011-12-06 Tue] - now running extractSprectum example again [2011-12-06 Tue] - setting default cache to 0, as cache=1 introduces unstabel behavious... will investigate that [2011-12-06 Tue] Changes in version 1.3.3 ------------------------ - added parallel computation for MSnExp quantitation using foreach with llply(..., .parallel=TRUE) [2011-12-03 Sat] - TODO document above in quantify-methods.Rd - added foreach and doMC in Suggests [2011-12-03 Sat] - added Spectrum removePeaks and clean'ing in readMSData [2011-12-05 Mon] Changes in version 1.3.2 ------------------------ - \dontrun{} extractSpectrum example, as this seems to be a major offender producing the intermittent check 'Error in function (x) : attempt to apply non-function' error [2011-11-07 Mon] - typo in Author@R [2011-11-14 Mon] - modified utils.removePeaks and utils.clean to call sapply instead of IRanges:sapply [2011-12-01 Thu] Changes in version 1.3.1 ------------------------ - Herve added BioGenerics as a dependency and import statement in NAMESPACE [2011-11-29 Tue] Changes in version 1.3.0 ------------------------ - Version bump for Bioc 2.10 devel Changes in version 1.2.0 ------------------------ - Version bump for Bioc 2.9 release Changes in version 1.1.28 ------------------------- - added pgfSweave to Suggests [2011-10-23 Sun] Changes in version 1.1.27 ------------------------- - fixed bug in readIspyData [2011-10-07 Fri] - removed (unexported) ratio code [2011-10-12 Wed] - added processing description when MSnSet['ing [2011-10-12 Wed] - man typos corrected [2011-10-14 Fri] - changed readMzXMLData to readMSData in tests [2011-10-14 Fri] - expecting warning for readMzXMLData in test_io [2011-10-14 Fri] Changes in version 1.1.26 ------------------------- - extractSpectra deprecated [2011-10-05 Wed] - small changes in cache.R functions [2011-10-05 Wed] - changed [, extractSpectra and extractPrecSpectra to update the .cache slot [2011-10-05 Wed] - MSnExp show method uses .cache when level==1. [2011-10-05 Wed] - Finished level 1 cache implementation: leads to an average 11.8 times faster MSnExp show method. [2011-10-05 Wed] Changes in version 1.1.25 ------------------------- - added .cache slot to pSet class [2011-10-03 Mon] - added pSet initialize method to set .cache and .cache$level as '0'. [2011-10-03 Mon] - Check that level is defined in .cache and env is locked in pSet validity method. [2011-10-03 Mon] - updated itraqdata.RData [2011-10-03 Mon] - Deprecated readMzXMLData, added defunct.Rd [2011-10-03 Mon] - changed readMzXMLData to readMSData in man [2011-10-03 Mon] - updated show MSnExp for speed [2011-10-03 Mon] - updated read*Data is support cache = [0|1]. [2011-10-03 Mon] - updated precScanNum to use sapply(spectra(...), precScanNum) instead of unlist(eapply(assayData(...), precScanNum)) to preserve splectra order. [2011-10-03 Mon] - new cache.R file with @.cache related code [2011-10-03 Mon] Changes in version 1.1.24 ------------------------- - in readMgfData, SCANS is not used to populate acquisitionNum anymore, as several scans might have been combined upstreams [2011-09-26 Mon] - added fillUp function in utils.R and exported [2011-09-27 Tue] - new MSnbase-io vignette [2011-09-28 Wed] Changes in version 1.1.23 ------------------------- - fixed writeMgfData("MSnExp") [2011-09-21 Wed] - readMgfData now works when mz and intensty are separated by a '\t' (as exported by PRIDE Inspector) [2011-09-21 Wed] - show("MSnExp") now works without retention time [2011-09-21 Wed] - updated mgf2Spectrum2 to make it faster [2011-09-21 Wed] - fixed missing fromFile slot in data created from readMgfData that prevented calling header [2011-09-21 Wed] - readMgfData now creates a fData based on the peak header [2011-09-21 Wed] - modified getCurveWidth to work with centroided data [2011-09-21 Wed] - fixed bug getCurveWidth [2011-09-21 Wed] Changes in version 1.1.22 ------------------------- - removed (internal) Mascot query link column in readIspyData to work with latest ouput version [2011-09-12 Mon] - removed the fillUp part in readIspyData [2011-09-14 Wed] - exported readIspyData [2011-09-20 Tue] - removed link to proteomics sig list [2011-09-20 Tue] - removed url in DESCRIPTION [2011-09-20 Tue] - Spectrum2 slot ms1scan renamed to precScanNum and populated using mzR::header()$precursorScanNum. Updated affected methods/functions and manual pages. New accessor method precScanNum is exported. THIS CHANGE IS NOT COMPATIBLE WITH PREVIOUSLY CREATED MSnSet -BJECTS! [2011-09-20 Tue] Changes in version 1.1.21 ------------------------- - updated write.exprs to add fData columns [2011-09-08 Thu] - added write.exprs and readMSnSet unit test [2011-09-08 Thu] Changes in version 1.1.20 ------------------------- - added a readMSnSet function [2011-09-08 Thu] - added a write.MSnSet("MSnSet") method [2011-09-08 Thu] - vignette/man updates - mainly data import section documenting readMSData and readMgfData [2011-09-08 Thu] - incorporating mzR io frame work [2011-09-05 Mon] - use mzR's peaksCount and header generics [2011-09-05 Mon] - added test to check that readMzXMLData and readMSData give same output [2011-09-05 Mon] - added readMSData.Rd doc file [2011-09-05 Mon] - added Author@R field in DESCRIPTION [2011-09-07 Wed] - compressed/resaved (using resaveRdaFiles) itraqdata.RData file to [2011-09-07 Wed] Changes in version 1.1.18 ------------------------- - read support for mgf files contributed by Guangchuang Yu [2011-07-06 Wed] - added as.ExpressionSet.MSnSet and setAs methods and updated MSnSet doc [2011-07-09 Sat] - fixed read/write mgf compatibility [2011-09-01 Thu] - added mgf io test [2011-09-01 Thu] - exported and document mfg read/write support [2011-09-01 Thu] - added centroided parameter to rawToSpectrum[1|2] to set this directly at object creation in readMzXmlData [2011-09-01 Thu] - other minor changes in Rd files [2011-09-01 Thu] - added warning checks for combineFeatures when verbose=TRUE in test_MSnSet.R [2011-09-02 Fri] Changes in version 1.1.17 ------------------------- - updated itraqdata manual [2011-06-27 Mon] - fixed bug in MSnSet validity method - msg was initialised to NULL when testing Biobase:::isValidVersion and Biobase::assayDataValidMembers [2011-07-02 Sat] - added t.MSnSet method [2011-07-02 Sat] - document t.MSnSet method [2011-07-05 Tue] - test for t-MSnSet [2011-07-05 Tue] - new "["-MSnSet method to properly subset qual slot [2011-07-06 Wed] - updated MSnSet validity method to check qual dims [2011-07-06 Wed] - combineFeatures now drops the spectrum-specific qual slot [2011-07-06 Wed] - test for "["-MSnSet [2011-07-06 Wed] Changes in version 1.1.16 ------------------------- - added addVigs2WinMenu call in .onAttach [2011-06-26 Sun] - added plotMzDelta paragraph in vignette [2011-06-26 Sun] Changes in version 1.1.15 ------------------------- - new names and description methods for ReporterIons [2011-06-16 Thu] - added validObject() checks [2011-06-16 Thu] - new removeReporters method [2011-06-16 Thu] - plotMzDelta is exported and documented [2011-06-17 Fri] Changes in version 1.1.14 ------------------------- - Adding plotMzDelta QC plot (not yet exported), contributed by Guangchuang Yu [2011-06-14 Tue] - created a locked environment to store amino.acids dataframe [2011-06-14 Tue] - TODO plotMzDelta documentation and vignette section - man DONE in v 1.1.15 , vignette DONE in v 1.1.16 Changes in version 1.1.13 ------------------------- - changed pSet [[ method [2011-06-13 Mon] - additional updates pSet [[ method [2011-06-13 Mon] - added MSnExp subsetting error tests [2011-06-13 Mon] - created new plotting-dataframe.R file with former plotting utils functions, now renamed plot*.header [2011-06-13 Mon] Changes in version 1.1.12 ------------------------- - added invisible(NULL) to all show methods [2011-06-08 Wed] - added centroided argument to plot.MSnExp [2011-06-09 Thu] Changes in version 1.1.11 ------------------------- - harmonised MSnExp and Spectrum plot axes labels [2011-05-18 Wed] - Added plotting customisation section in vignette [2011-05-18 Wed] - updated signature of plot2d method to "MSnExp" only [2011-05-18 Wed] - added/exported plotDensity methods [2011-05-18 Wed] - started QC vignette section [2011-05-18 Wed] - added preprocSelection and preprocSelectionTable functions [2011-05-18 Wed] - TODO document preprocSelection[Table] in vignette - reduces plot2d-figure and plotDensity-figure sizes using png [2011-05-19 Thu] - added plotDensity doc [2011-05-19 Thu] - added round param to preprocSelection[Table] [2011-05-19 Thu] - preprocSelection[Table] documented and exported [2011-05-19 Thu] - fixed bug in plot.Spectrum1 [2011-05-24 Tue] - changed removePeaks setGeneric explicit signature [2011-05-26 Thu] - added MassSpectrometry biocView [2011-05-27 Fri] Changes in version 1.1.10 ------------------------- - minor updates in demo vignette [2011-05-13 Fri] - added plot argument to plot methods [2011-05-16 Mon] - fix in makeImpuritiesMatrix [2011-05-16 Mon] - added meanSdPlot MSnSet method [2011-05-17 Tue] - minor cosmetic fix in purityCorrect error message [2011-05-17 Tue] - added method="sum" to Spectrum/MSnExp normalisation [2011-05-17 Tue] - typo in MSnSet-class.Rd corrected [2011-05-17 Tue] Changes in version 1.1.9 ------------------------ - exporting normali[s|z]e methods for MSnSet, Spectrum and MSnExp [2011-05-12 Thu] - added quantile normalisation [2011-05-12 Thu] - added quantile.robust normalisation [2011-05-12 Thu] - added vsn2 normalisation [2011-05-12 Thu] - added normalise manual [2011-05-12 Thu] - included normalisation section in vignette [2011-05-13 Fri] - more vignette updates [2011-05-13 Fri] - updated plotting methods to round MZ in title [2011-05-13 Fri] Changes in version 1.1.8 ------------------------ - added writeMgfData method from spectra and experiment [2011-05-09 Mon] - added writeMgfData manual [2011-05-09 Mon] - added itraqdata data set and updated vignette to use it [2011-05-11 Wed] - updated man pages to use tiny dummyiTRAQ.mzXML [2011-05-11 Wed] - added makeImpuritiesMatrix function [2011-05-11 Wed] Changes in version 1.1.7 ------------------------ - reporter ions purity correction method, man and test [2011-05-09 Mon] - updated vignette [2011-05-09 Mon] Changes in version 1.1.6 ------------------------ - added incomplete dissociation and spectral counting sections to demo vignette [2011-05-06 Fri] - added bioc-sig-proteomics link to foreword [2011-05-06 Fri] - type in foreword [2011-05-06 Fri] Changes in version 1.1.5 ------------------------ - added combineFeatures example in demo vignette [2011-05-05 Thu] Changes in version 1.1.4 ------------------------ - readIspyData updated to return updated factors [2011-05-03 Tue] - added unexported/undocumented combineFeatures function for MSnSets [2011-05-03 Tue] - added basic tests for combineFeatures [2011-05-03 Tue] - added combineFeatures manual [2011-05-04 Wed] - exportig combineFeatures [2011-05-04 Wed] Changes in version 1.1.3 ------------------------ - as.data.frame.Spectrum columns now are (first) mz and (second) intensity [2011-04-27 Wed] - exporting as.data.frame.Spectrum and coerce [2011-04-27 Wed] Changes in version 1.1.2 ------------------------ - Simplified quantify generic signature - now only object argument [2011-04-19 Tue] - Added strict parameter to quantify method, man updated, added relevant test - Added illustrative plot for quantitation methods in MSnbase-demo vignette [2011-04-19 Tue] - Added illustrative plot for data pre-processing (removePeaks and clean) in MSnbase-demo vignette [2011-04-20 Wed] - No warnings are issued anymore when peaks expands outside of mz(reporters) +/- width(reporters). See ?quantify on how to check this manually. [2011-04-19 Tue] - No warnings are issued anymore when reporter peaks are missing. See ?quantify on how to check this manually. [2011-04-20 Wed] - pSet validity warns if length(unique(msLevel(object))) ] 1, rather than != 1. The latter triggered a warning for a new("MSnExp"). [2011-04-20 Wed] Changes in version 1.1.1 ------------------------ - added setAs data.frame and as.data.frame methods for Spectrum objects [2011-03-29 Tue] - support for uncentroided MS2 spectra plots [2011-03-31 Thu] [2011-04-02 Sat] - support for uncentroided MS1 spectra plots [2011-04-02 Sat] - minor modification to readIspyData [2011-04-04 Mon] - removed centroided slot from MSnProcess and added to individial Spectrum instances. Relevant for Velos HCD (profile)/CID (uncentroided) data [2011-04-04 Mon] - modified readMzXmlData accordingly [2011-04-04 Mon] - added validObject(new(...)) tests for each class [2011-04-04 Mon] - added centroided[<-] methods to Spectrum and pSet [2011-04-04 Mon] - added 'keepAll' parameter to readIspyData [2011-04-11 Mon] Changes in version 0.99.4 ------------------------- - removed pgfSweave from Suggests field [2011-04-04 Mon] Changes in version 0.99.3 ------------------------- - Using Sweave rather than pgfSweave to build on lamb1. [2011-03-28 Mon] Changes in version 0.99.2 ------------------------- - updated references in package Rd [2011-03-24 Thu] - added readIspyData.Rd [2011-03-24 Thu] - removed old readMzXMLData function [2011-03-24 Thu] - cleaning up code [2011-03-24 Thu] - fixed MSnSet initialize: setting experimentData as MIAPE [2011-03-25 Fri] - fixed MSnSet initialize: identical featureNames in assayData and featureData for empty MSnExp istances [2011-03-25 Fri] - better test organisation and added object validity tests [2011-03-25 Fri] - updated readIspyData function [2011-03-25 Fri] Changes in version 0.99.1 ------------------------- - fake vignettes are copied back in inst/doc/. to make sur tar tarball can be extracted and build again [2011-03-24 Thu] - Making clean after make all [2011-03-24 Thu] Changes in version 0.99.0 ------------------------- - MSnProcess@process get's one line when subsetting and MSnExp object [2011-03-21 Mon] - Updated vignette Makefile [2011-03-22 Tue] - Added fake vignettes [2011-03-22 Tue] - Version set to 0.99.0 [2011-03-22 Tue] - Minor changes in quantify-method.Rd [2011-03-22 Tue] - added .Rbuildignore to ignore 'sweave-cache.*' [2011-03-22 Tue] - added R/zzz.R with start-up message [2011-03-23 Wed] - Added width generic [2011-03-23 Wed] - IRanges in now imported [2011-03-23 Wed] Changes in version 0.2.0 [2011-03-17 Thu] ----------------------------------------- - MSnSet now extends eSet, reimplementing the ExpressionSet class with exception of the experimentData slot, that must now be a MIAPE instance. - updated MIAPE substantially and added accessor methods. - updated docs and vignettes to reflect above changes. Changes in version 0.1.5 ------------------------ - added zoo to Suggest, as zoo::rollapply is used in vignette. - changes rollapply call to zoo:::rollapply.zoo, to make it work with zoo_1.6-4, rather that depending on zoo_1.7-0, which is not yet on CRAN (only r-forge). - added vns to Suggests, as it is used in the demo vignette. Changes in version 0.1.4 ------------------------ - added pgfSweave to Suggests, as is called in vignette Makefile Changes in version 0.1.3 ------------------------ - Updates to ReporterIons man page - Moved some Depends to Imports and updated NAMESPACE - corrected a IRanges:::sapply ot IRanges::sapply in utils.R - added inst/tests/test_MSnProcess.R Changes in version 0.1.2 ------------------------ - MSnProcess@MSnbaseVersion is not set in the initialize method instead to the prototype - changed R CMD to $(R_HOME)/bin/R CMD in inst/doc/Makefile - removed first and last (was 5th) MS1 spectra and associated MS2 spectra from dummy file to reduce size below 2MB. - Updated tests to reflect new dummy data set - Edition of dummy brakes readMzXMLData with msLevel=1 -- comment related tests - Updated MSnbase-demo vignette and man to use good spectra un plots (i.e "X43" instead of "X64") Changes in version 0.1.1 ------------------------ - Added LazyLoad: yes in DESCRIPTION and modified docs accordingly - Added NEWS file Changes in version 0.1.0 ------------------------ - Added MSnbase-demo vignette - Added MSnbase-development vignette