CHANGES IN VERSION 2.0.2 ------------------------ o Add option sortMethod that defaults to "auto" on R < 3.3 and "radix" otherwise. CHANGES IN VERSION 2.0.1 ------------------------ o Update readMSnSet2 to save filename <2016-11-09 Wed> o 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 2.0.0 ------------------------ o New version for Bioconductor release version 3.4 CHANGES IN VERSION 1.99.6 ------------------------- o Reverting to old initialize,Spectrum (see issue #163) <2016-10-07 Fri> o 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 ------------------------- o Add removeReporters,OnDiskMSnExp (see issue #161 for details) <2016-10-07 Fri> CHANGES IN VERSION 1.99.4 ------------------------- o Fix bug in readMzTabData_v0.9 <2016-10-07 Fri> CHANGES IN VERSION 1.99.3 ------------------------- o 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 ------------------------- o Added isolationWindow,MSnExp method <2016-09-23 Fri> o Updated readMSData Spectrum2 class to support MS levels > 2 <2016-09-30 Fri> CHANGES IN VERSION 1.99.1 ------------------------- o Fix MS level test in quantify,OnDiskMSnExp to support MS2+ level quantitation <2016-09-14 Wed> CHANGES IN VERSION 1.99.0 ------------------------- o Add normalize method for OnDiskMSnExp <2016-06-07 Tue>. o Fix bug in readMSData <2016-06-07 Tue>. o Added documentation and unit test for trimMz <2016-06-01 Wed>. o Added trimMz method for OnDiskMSnExp objects <2016-05-31 Tue>. o 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>. o Added a section to the MSnbase-development vignette <2016-05-27 Fri>. o Finished with all pSet inherited methods and docs <2016-05-26 Thu>. o Added rtlim argument to spectra method for OnDiskMSnExp <2016-05-26 Thu>. o Methods rtime, tic, ionCount, polarity and acquisitionNum implemented <2016-05-25 Wed>. o Documentation added for most methods <2016-05-25 Wed>. o Methods peaksCount and spectra for OnDiskMSnExp objects implemented <2016-05-24 Tue>. o Performance and validation tests for the Spectrum1 C-constructor <2016-05-23 Mon>. o Spectrum1 constructor implemented in C (presently not exported) <2016-05-20> o length, scanIndex, acquisitionNum and centroided implemented <2016-05-20> o Implemented fromFile and msLevel for OnDiskMSnExp <2016-05-19 Thu> o Implemented an OnDiskMSnExp class for on-the-fly data import <2016-05-19 Thu> o Fixed the validate method for pSet to play nicely with OnDiskMSnExp objects <2016-05-19 Thu> o 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> o Implemented a ProcessingStep class that helps to keep track how (spectra) data should be processed on the fly <2016-05-18 Wed> o In OnDiskMSnExp validity, check that the assaydata is empty <2016-06-28 Tue> o Pass neutralLoss in plot,Spectrum,Spectrum-method to .calculateFragments; fixes #146 <2016-08-12 Fri> o Allow the user to specify the `cex`, `lwd`, `pch` for peaks and fragments in plot,Spectrum,Spectrum-method; closes #148 <2016-08-12 Fri> o Update centroided with an na.fail argument (see issue #150 for details) <2016-08-12 Fri> o Fix warning in readMgfData if TITLE contains multiple "=" <2016-08-24 Wed> CHANGES IN VERSION 1.21.8 ------------------------- o Update MSnSet validity method to guard agains empty string feature names <2016-06-20 Mon> o Simplify show,MSnExp method to work for various MS level cases and OnDiskMSnExp - addressed issue #98 <2016-06-28 Tue> o removeMultipleAssignment also removes features that were not assigned (i.e. that have fcol (nprots) NA) <2016-07-02 Sat> o New smoothed slot/accessor/replacement methods <2016-07-08 Fri> o Update reporter masses and add TMT10 ETD/HCD <2016-07-20 Wed> o returning empty spectrum when fliterMz has empty range - see issue #134 <2016-07-22 Fri> o (mz, intensity) values are reordered based on order(mz) - see issue #135 <2016-07-26 Tue> o fix bug in bin,Spectrum - see issue #137 <2016-08-05 Fri> CHANGES IN VERSION 1.21.7 ------------------------- o Update iPQF reference <2016-06-01 Wed> o 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. o readMSData: if no phenodata is provided it creates an empty one with rownames corresponding to the file names. See PR #91. o Lock itraqdata's assaydata bindings <2016-06-08 Wed> CHANGES IN VERSION 1.21.6 ------------------------- o MSmap unit test <2016-05-23 Mon> o Fix bug in as(MSmap, "data.frame") <2016-05-23 Mon> CHANGES IN VERSION 1.21.5 ------------------------- o Added Johannes as contributor <2016-05-12 Thu> o Deprecate MzTab v0.9 <2016-05-19 Thu> o Fix old googlecode URLs to old MzTab <2016-05-19 Thu> CHANGES IN VERSION 1.21.4 ------------------------- o More MzTab and Spectrum1 unit testing <2016-05-08 Sun> o Speed up readMSData (PR #86 by jotsetung) <2016-05-12 Thu> o Replace example file URL to use github instead of googlecode <2016-05-12 Thu> CHANGES IN VERSION 1.21.3 ------------------------- o No fileNames replacement method <2016-05-07 Sat> o fileNames unit tests <2016-05-07 Sat> o add fileNames to class that had fileName accessor (MSmap, MzTab) <2016-05-07 Sat> CHANGES IN VERSION 1.21.2 ------------------------- o Check for rownames/fnames in readMSnSet2 and unit test <2016-05-05 Thu> CHANGES IN VERSION 1.21.1 ------------------------- o Fix wrong indexing in readMSdata, msLevel==1 (PR #85 by jotsetung) <2016-05-04 Wed> o grep/getEcols have a 'n' param specifying which line to grep/get <2016-05-04 Wed> CHANGES IN VERSION 1.21.0 ------------------------- o Version bump for new Bioc devel CHANGES IN VERSION 1.20.0 ------------------------- o Version bump for Bioc release version 3.3 CHANGES IN VERSION 1.19.24 -------------------------- o more unit tests and bug fixes <2016-04-30 Sat> <2016-05-02 Mon> CHANGES IN VERSION 1.19.23 -------------------------- o more unit tests and bug fixes <2016-04-27 Wed> <2016-04-28 Thu> CHANGES IN VERSION 1.19.22 -------------------------- o more unit tests <2016-04-23 Sat> <2016-04-24 Sun> <2016-04-26 Tue> o remove readIspyData functions <2016-04-23 Sat> o Fixed bug in error catching in utils.mergeSpectraAndIdentificationData <2016-04-23 Sat> CHANGES IN VERSION 1.19.21 -------------------------- o nadata.R unit tests and bugs fixed <2016-04-22 Fri> CHANGES IN VERSION 1.19.20 -------------------------- o Moved makeNaData[2] and whichNA (was in pRoloc) <2016-04-21 Thu> CHANGES IN VERSION 1.19.19 -------------------------- o 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 -------------------------- o fix typo in man <2016-04-02 Sat> CHANGES IN VERSION 1.19.17 -------------------------- o 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 -------------------------- o add estimateNoise,[Spectrum|MSnExp]-method; closes #78 <2016-03-10> o 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 -------------------------- o limit readMSData unit test due to Windows-only error <2016-03-09 Wed> o fix unit test for utils.colSd(x, na.rm=TRUE) CHANGES IN VERSION 1.19.14 -------------------------- o Document change in nQuants param fcol to groupBy <2016-03-02 Wed> CHANGES IN VERSION 1.19.13 -------------------------- o Fixed bug in bin_Spectrum, reported by Weibo Xie <2016-02-16 Tue> o Added unit test for bug above <2016-02-16 Tue> o Merged 'apply functions columnwise by group' <2016-02-16 Tue> o 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 -------------------------- o 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 -------------------------- o Fix trimws generic/methods with useAsDefault (see issue #75) <2016-02-02 Tue> o add exprs,MSnSet-method alias (since exprs is now exported) <2016-02-02 Tue> CHANGES IN VERSION 1.19.10 -------------------------- o export exprs, fvarLabels, and sampleNames[<-] <2016-01-30 Sat> CHANGES IN VERSION 1.19.9 ------------------------- o new trimws method for data.frames and MSnSets <2016-01-29 Fri> CHANGES IN VERSION 1.19.8 ------------------------- o readMSnSet2 now also accepts a data.frame as input <2016-01-29 Fri> o selective ggplot2 import <2016-01-29 Fri> CHANGES IN VERSION 1.19.7 ------------------------- o new sampleNames<- for pSet and MSnExp objects <2015-12-15 Tue> o Fix bug preventing to write MS1 to mgf (fixes issue #73 reported by meowcat) <2015-12-18 Fri> CHANGES IN VERSION 1.19.6 ------------------------- o MSnExp feautreNames are now X01, X02 (0 after X) to maintain numerical sorting of ASCII characters; contributed by sgibb <2015-12-14 Mon> o 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 ------------------------- o 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 ------------------------- o Replacement method for MSnSetList names <2015-11-24 Tue> CHANGES IN VERSION 1.19.3 ------------------------- o New argument fcol to selectFeatureData to select feature variables using a vector <2015-10-28 Wed> CHANGES IN VERSION 1.19.2 ------------------------- o new selectFeatureData function to subset the feature data <2015-10-24 Sat> CHANGES IN VERSION 1.19.1 ------------------------- o Remove generics that are defined in ProtGenerics <2015-10-15 Thu> CHANGES IN VERSION 1.19.0 ------------------------- o Bioc devel 3.3 CHANGES IN VERSION 1.18.0 ------------------------- o Bioc release 3.2 CHANGES IN VERSION 1.17.16 -------------------------- o new default parameter 'feature weight' in iPQF by Martina Fisher (see PR#65) <2015-10-07 Wed> CHANGES IN VERSION 1.17.15 -------------------------- o Fix typo in plot man <2015-08-23 Sun> CHANGES IN VERSION 1.17.14 -------------------------- o Fix typo in impute man <2015-08-17 Mon> CHANGES IN VERSION 1.17.13 -------------------------- o partly rewrite writeMgfData <2015-05-16 Thu> o initial hmap function <2015-07-16 Thu> o fix bug in plotting MS1 spectra (closes issue #59) <2015-07-16 Thu> o new image implementation, based on @vladpetyuk's vp.misc::image_msnset <2015-07-25 Sat> o 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 -------------------------- o fix show MIAPE when some otherInfo at NA <2015-07-15 Wed> CHANGES IN VERSION 1.17.11 -------------------------- o adding unit tests <2015-07-01 Wed> o fix abundance column selection when creating MSnSet form MzTab <2015-07-01 Wed> o new mzTabMode and mzTabType shortcut accessors for mode and type of an mzTab data <2015-07-01 Wed> CHANGES IN VERSION 1.17.10 -------------------------- o Fix URL <2015-06-30 Tue> CHANGES IN VERSION 1.17.9 ------------------------- o calculateFragments' "neutralLoss" argument is now a list (was a logical before), see #47. <2015-06-24 Wed> o add defaultNeutralLoss() function to fill calculateFragments' modified "neutralLoss" argument, see #47. <2015-06-24 Wed> CHANGES IN VERSION 1.17.8 ------------------------- o coercion from IBSpectra to MSnSet, as per user request <2015-06-23 Tue> o new iPQF combineFeature method <2015-06-24 Wed> CHANGES IN VERSION 1.17.7 ------------------------- o Fix support of identification-only mzTab files <2015-06-22 Mon> CHANGES IN VERSION 1.17.6 ------------------------- o Export metadata,MzTab-method <2015-06-19 Fri> o Replace spectra,MzTab-method by psms,MzTab-method <2015-06-20 Sat> o 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> o calculateFragments gains the feature to handle N-/C-terminal modifications, see #47. <2015-06-21 Sun> o update readMzTabData example <2015-06-22 Mon> CHANGES IN VERSION 1.17.5 ------------------------- o 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 ------------------------- o New lengths method for FoICollection instances <2015-06-06 Sat> o New image2 function for matrix object, that behaves like the method for MSnSets <2015-06-10 Wed> o image,MSnSet labels x and y axis as Samples and Features <2015-06-10 Wed> o fixed bug in purityCorrect, reported by Dario Strbenac <2015-06-11 Thu> CHANGES IN VERSION 1.17.3 ------------------------- o iTRAQ 8-plex correction factors and impurity matrix <2015-05-22 Fri> CHANGES IN VERSION 1.17.2 ------------------------- o new filterZero function <2015-05-01 Fri> CHANGES IN VERSION 1.17.1 ------------------------- o new MSnSetList class <2015-04-19 Sun> o new commonFeatureNames function <2015-04-14 Tue> o new compareMSnSets function <2015-04-19 Sun> o splitting and unsplitting MSnSets/MSnSetLists <2015-04-19 Sun> CHANGES IN VERSION 1.17.0 ------------------------- o new devel version for Bioc 3.2 CHANGES IN VERSION 1.15.18 -------------------------- o fix failing test_MSnExp::readMSData unit test on Windows i386 (@.cache$size being different on that arch) [2015-04-14 Tue] o merge @vladpetyuk PR #50 fix of combine features bug [2015-04-14 Tue] CHANGES IN VERSION 1.15.17 -------------------------- o add TMT10 paragraph and fig to demo vignette [2015-04-09 Thu] CHANGES IN VERSION 1.15.16 -------------------------- o support for TMT10 plex [2015-04-08 Wed] CHANGES IN VERSION 1.15.15 -------------------------- o using serial parallelisation during quantitation in unit tests [2015-04-02 Thu] CHANGES IN VERSION 1.15.14 -------------------------- o 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 -------------------------- o improve nbavg imputation description and add example [2015-03-22 Sun] o reduce compareSpectra example timing [2015-03-30 Mon] CHANGES IN VERSION 1.15.12 -------------------------- o average neighbour imputation for ordered fractions along a gradient [2015-03-21 Sat] CHANGES IN VERSION 1.15.11 -------------------------- o update malformed Description [2015-03-20 Fri] CHANGES IN VERSION 1.15.10 -------------------------- o update compareSpectra man [2015-03-19 Thu] o ExpressionSet <-> MSnSet coercion [2015-03-19 Thu] CHANGES IN VERSION 1.15.9 ------------------------- o use S4Vectors' isEmpty generic [2015-03-10 Tue] CHANGES IN VERSION 1.15.8 ------------------------- o Improved imputation section in demo vignette [2015-03-05 Thu] CHANGES IN VERSION 1.15.7 ------------------------- o Importing ProtGenerics [2015-02-28 Sat] o selective import of MALDIquant [2015-03-02 Mon] CHANGES IN VERSION 1.15.6 ------------------------- o add intensity column to the calculateFragments output; closes #47;1 [2015-02-02 Mon] o 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] o add neutralLoss argument to calculateFragments and calculate loss of water and ammonia; closes #47:3 [2015-02-19 Thu] o new imputation methods via imputeLCMD and norm [2015-02-09 Mon] o vignette updates [2015-02-09 Mon] o imputation unit test [2015-02-24 Tue] CHANGES IN VERSION 1.15.5 ------------------------- o update dependency to mzID >= 1.5.2 [2015-01-28 Wed] o rewrite addIdentificationData and change its signature [2015-01-28 Wed] o 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] o add a section about MSmaps in the vignette [2015-02-02 Mon] o 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 ------------------------- o partly rewrite readMgfData [2015-01-19 Mon] o Typo in addIdentification data man [2015-01-20 Tue] o use Biocstyle [2015-01-23 Fri] o replace require with requireNamespace [2015-01-23 Fri] CHANGES IN VERSION 1.15.3 ------------------------- o plot,Spectrum2,character to add fragment ions based on peptide sequence [2014-11-20 Thu] o update vignette with above [2014-11-20 Thu] o comment parallel code in quantify man [2015-01-09 Fri] CHANGES IN VERSION 1.15.2 ------------------------- o merged sgibb's pull request exporting overloaded methods as well [2014-11-02 Sun] o updated MSnSet validity, checking that exprs(.) is a matrix [2014-11-12 Wed] o fix error (missing header extraction) is MSmap example [2014-11-18 Tue] CHANGES IN VERSION 1.15.1 ------------------------- o 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 ------------------------- o Devel version for Bioc 3.1 CHANGES IN VERSION 1.14.0 ------------------------- o Release version for Bioc 3.0 CHANGES IN VERSION 1.13.16 -------------------------- o width generic if non-existant [2014-09-03 Wed] o fix undocumented S4 methods warnings [2014-09-27 Sat] CHANGES IN VERSION 1.13.15 -------------------------- o msMap(MSmap)<- method [2014-08-12 Tue] o Typo in MIAPE man [2014-08-29 Fri] CHANGES IN VERSION 1.13.14 -------------------------- o Fix xic example [2014-08-08 Fri] o importing lattice, ggplot2 (was depends) and suggesting rgl [2014-08-09 Sat] o MSmap infrastructure [2014-08-09 Sat] CHANGES IN VERSION 1.13.13 -------------------------- o fix issue with readMSnSet2 without fdata [2014-07-28 Mon] CHANGES IN VERSION 1.13.12 -------------------------- o Don't import width from IRanges [2014-07-23 Wed] o qual slot is populated again [2014-07-23 Wed] CHANGES IN VERSION 1.13.11 -------------------------- o remove Vennerable::Venn from example and DESCRIPTION [2014-06-19 Thu] CHANGES IN VERSION 1.13.10 -------------------------- o new averageMSnSet function to generate an average over a list of MSnSets. [2014-06-17 Tue] o new non-parametric coefficent of variation function [2014-06-17 Tue] o Using/importing IRanges::width [2014-06-18 Wed] CHANGES IN VERSION 1.13.9 ------------------------- o new listOf helper function [2014-06-16 Mon] o compfnames to compare and document differences in MSnSet feature names [2014-06-16 Mon] o suggesting Vennerable (compfnames example) and roxygen2 (generate rd) [2014-06-16 Mon] CHANGES IN VERSION 1.13.8 ------------------------- o Add recommended biocView [2014-06-05 Thu] CHANGES IN VERSION 1.13.7 ------------------------- o Bug tracking link [2014-05-26 Mon] CHANGES IN VERSION 1.13.6 ------------------------- o new isEmpty method for Spectrum instances [2014-05-14 Wed] o removePeaks does not try for empty Spectra [2014-05-14 Wed] o isEmpty unit test [2014-05-14 Wed] CHANGES IN VERSION 1.13.5 ------------------------- o export .get.amino.acids function [2014-05-08 Thu] o removePeaks for centroided data [2014-05-08 Thu] o add new exported function get.atomic.mass [2014-05-08 Thu] o Spectrum[2] prototype sets centroided=FALSE by default (instead of logical()) [2014-05-08 Thu] o fnamesIn also supports y = "data.frame" [2014-05-14 Wed] o Using BiocParallel for parallel support; replaced parallel argument with BPPARAM [2014-05-14 Wed] CHANGES IN VERSION 1.13.4 ------------------------- o Document difference between traceable and non-traceable FeaturesOfInterest instances [2014-04-30 Wed] o ignoring desciptions with length > 1 [2014-04-30 Wed] CHANGES IN VERSION 1.13.3 ------------------------- o FeaturesOfInterest [2014-04-29 Tue] CHANGES IN VERSION 1.13.2 ------------------------- o add compareSpectra to compare Spectrum objects [2014-04-09 Wed] o add bin method for Spectrum objects [2014-04-09 Wed] o recreate inst/extdata/msx.rda for R 3.1 and Biobase 2.24 [2014-04-13 Sun] o add plot,Spectrum,Spectrum method [2014-04-14 Mon] o add calculateFragments,character,Spectrum and calculateFragments,character,missing methods [2014-04-15 Tue] o updated readMSData test unit to ignore object@.__classVersion__ that fails with latest R/Bioc versions [2014-04-15 Tue] o formatRt conversion from 'mm:sec' to sec and unit test [2014-04-17 Thu] o 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 ------------------------- o add precursor method to Spectrum2 normalisation method [2014-04-08 Tue] o add smooth for MSnExp and Spectrum classes [2014-04-10 Thu] o add pickPeaks for MSnExp and Spectrum classes [2014-04-10 Thu] o updated show,MSnExp to display only first/last files when > 2 [2014-04-11 Fri] CHANGES IN VERSION 1.13.0 ------------------------- o New devel version for Bioc 3.0 CHANGES IN VERSION 1.11.14 -------------------------- o update dependency to R >= 3.1 [2014-04-05 Sat] CHANGES IN VERSION 1.11.13 -------------------------- o Document [get|grep]Ecols in io vignette [2014-03-31 Mon] o typo in readMSnSet man [2014-03-31 Mon] o updated affiliation in vignettes [2014-03-31 Mon] CHANGES IN VERSION 1.11.12 -------------------------- o Fixed a bug in readMzTabData reported by Hendrik Weisser [2014-03-26 Wed] CHANGES IN VERSION 1.11.11 -------------------------- o precomputed msx test data now has id data [2014-03-25 Tue] o quantitation unit tests [2014-03-25 Tue] o quantify method now accepts label-free methods [2014-03-25 Tue] CHANGES IN VERSION 1.11.10 -------------------------- o import mzID [2014-03-20 Thu] o dummyiTRAQ id extdata [2014-03-21 Fri] o add addIdentificationData method for MSnExp and MSnSet [2014-03-21 Fri] o using data from pRolocdata (was pRoloc) [2014-03-23 Sun] o added removeNoId,MSnExp,MSnSet methods [2014-03-23 Sun] o added idSummary,MSnExp,MSnSet methods [2014-03-24 Mon] o 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] o NAnnotatedDataFrame now has default multiplex 1 [2014-03-25 Tue] o NAnnotatedDataFrame unit tests [2014-03-25 Tue] CHANGES IN VERSION 1.11.9 ------------------------- o write.exprs can have fDataCol or fcol (for consistence) [2014-03-17 Mon] o Fixing bug in combineFeatures(..., is.character(groupBy)) [2014-03-19 Wed] o fixed combineFeatures [2014-03-20 Thu] o added example, test and doc for combineFeatures with list [2014-03-20 Thu] CHANGES IN VERSION 1.11.8 ------------------------- o adding redundancy handling to combineFeatures (by vladpetyuk, pull request #18) [2014-03-14 Fri] o updated combineFeatures signature to accomodate above changes [2014-03-14 Fri] o updated unit tests for new testhat 0.8 [2014-03-14 Fri] CHANGES IN VERSION 1.11.7 ------------------------- o NA CHANGES IN VERSION 1.11.6 ------------------------- o add corresponding xcms functions to the chromatogram and xic manual page [2014-02-21 Fri] o new bpca imputation methods [2014-02-27 Thu] o replacing stop_on_error with option in vignette [2014-02-27 Thu] CHANGES IN VERSION 1.11.5 ------------------------- o typo in MSnSet droplevels man [2014-01-27 Mon] o typo in MSnbase-demo vignette [2014-02-20 Thu] o fix BPI legend in chromatogram [2014-02-20 Thu] CHANGES IN VERSION 1.11.4 ------------------------- o passing ... to sweep when normalising [2013-12-08 Sun] o updated makeMTD to accomodate new MS ontology [2013-12-23 Mon] CHANGES IN VERSION 1.11.3 ------------------------- o updated mzTab example files to new url [2013-11-15 Fri] o warning about mzTab versions [2013-11-15 Fri] CHANGES IN VERSION 1.11.2 ------------------------- o move inst/doc to vignettes [2013-10-19 Sat] CHANGES IN VERSION 1.11.1 ------------------------- o document na.rm in combineFeatures Rd [2013-10-18 Fri] CHANGES IN VERSION 1.11.0 ------------------------- o New devel version for Bioc 2.14 CHANGES IN VERSION 1.9.12 ------------------------- o fix MSnSet -] ExpressionSet [2013-10-13 Sun] o MSnSet -] ExpressionSet unit test [2013-10-13 Sun] CHANGES IN VERSION 1.9.11 ------------------------- o MIAPE to MIAME conversion [2013-10-11 Fri] o proper MIAME when MSnSet -] ExpressionSet [2013-10-11 Fri] CHANGES IN VERSION 1.9.10 ------------------------- o faster plotMzDelta [2013-09-28 Sat] o faster plotMzDelta for mzRramp instances [2013-09-29 Sun] o chromatogram method [2013-10-04 Fri] o plotMzDelta has subset arg [2013-10-04 Fri] o xic method [2013-10-04 Fri] o suggesting msdata for chromatogram example [2013-10-04 Fri] o renamed plotting arg 'centroided.' [2013-10-04 Fri] CHANGES IN VERSION 1.9.9 ------------------------ o typo in filterNA Rd [2013-09-18 Wed] o writeMgfData now has a progress bar [2013-09-24 Tue] o centroided(MSnExp) <- TRUE now allowed [2013-09-24 Tue] CHANGES IN VERSION 1.9.8 ------------------------ o using new.env(parent=emptyenv()) to get rid of enclosing env when creating new MSnExps [2013-09-17 Tue] o new (private) MSnExp.size function [2013-09-17 Tue] CHANGES IN VERSION 1.9.7 ------------------------ o Passing ... to read.table in MSnbase:::readIspy[Silac|15N]Data [2013-09-16 Mon] o QualityControl biocView [2013-09-16 Mon] CHANGES IN VERSION 1.9.6 ------------------------ o new as.data.frame.MSnSet method [2013-08-16 Fri] o new ms2df function [2013-08-16 Fri] o new getEcols and grepEcols helpers for readMSnSet2 [2013-08-16 Fri] CHANGES IN VERSION 1.9.5 ------------------------ o typo in Author[s]@R [2013-05-15 Wed] CHANGES IN VERSION 1.9.4 ------------------------ o new simple MSnSet constructor [2013-05-07 Tue] CHANGES IN VERSION 1.9.3 ------------------------ o Using knitr as VignetteEngine [2013-04-29 Mon] o Remove LazyLoad from DESCRIPTION, which is default nowadays [2013-04-29 Mon] o knitr dependency ] 1.1.0 for VignetteBuilder [2013-04-29 Mon] o Adding MSnSet creating sections in io vignette [2013-04-29 Mon] o new readMSnSet2 function [2013-04-30 Tue] CHANGES IN VERSION 1.9.2 ------------------------ o clean has now a all param (default FALSE is retain original behavious) to remove all 0 intensity values [2013-04-17 Wed] o using BiocGenerics::normalize [2013-04-25 Thu] CHANGES IN VERSION 1.9.1 ------------------------ o new logging utility function to update an MSnSet's processingData(object)$processing [2013-03-29 Fri] o Proper logging in t.MSnSet [2013-03-29 Fri] CHANGES IN VERSION 1.9.0 ------------------------ o new Bioc 2.13 devel version CHANGES IN VERSION 1.8.0 ------------------------ o new Bioc 2.12 stable version CHANGES IN VERSION 1.7.25 ------------------------- o 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 ------------------------- o Mention scale in vignette [2013-03-02 Sat] o exprsToRatio matrix method [2013-03-20 Wed] CHANGES IN VERSION 1.7.23 ------------------------- o new private nologging function [2013-02-21 Thu] o adding total number of features on plotNA [2013-02-22 Fri] o updated msnbase.r [2013-02-26 Tue] CHANGES IN VERSION 1.7.22 ------------------------- o msnbase.r na.rm arg [2013-02-20 Wed] CHANGES IN VERSION 1.7.21 ------------------------- o Added impute method [2013-02-19 Tue] CHANGES IN VERSION 1.7.20 ------------------------- o Explicitating that normalise and normalize are the same methods in the man. [2013-02-13 Wed] CHANGES IN VERSION 1.7.19 ------------------------- o adding MIAPE and pSet accessors: analyserDetails, analyzerDetails, ionSourceDetails, instrumentModel, instrumentManufacturer, instrumentCustomisations [2013-02-12 Tue] o switching back to analyserDetails slot [2013-02-12 Tue] CHANGES IN VERSION 1.7.18 ------------------------- o readMgfData now supports comments and PEPMASS with precursor mz and intensity, requested by Thomas Taus [2013-02-11 Mon] o improved and running read/writeMgfData example [2013-02-11 Mon] o new scanIndex accessor method [2013-02-11 Mon] CHANGES IN VERSION 1.7.17 ------------------------- o added a analyzer accessors/slot to accomodate new mzTab files with more meta-data [2013-01-30 Wed] CHANGES IN VERSION 1.7.16 ------------------------- o fixing knitr 1.0 compatibility [2013-01-15 Tue] CHANGES IN VERSION 1.7.15 ------------------------- o new scale method [2013-01-11 Fri] o renaming scale.mean and scale.median normalisation methods to center.mean and centre.median [2013-01-11 Fri] CHANGES IN VERSION 1.7.14 ------------------------- o new unexported readIspy15NData [2013-01-09 Wed] o min.int readIspy[Silac|15N]Data arg [2013-01-11 Fri] CHANGES IN VERSION 1.7.13 ------------------------- o msnbase.r v0.1.1 with -h (help) arg [2013-01-08 Tue] o msnbase.r coerce -b arg to numeric [2013-01-08 Tue] o testing if any features left in readIspyData [2013-01-08 Tue] CHANGES IN VERSION 1.7.12 ------------------------- o updated makeImpuritiesMatrix to create matrix from csv file with correction factors [2012-12-23 Sun] o makeImpuritiesMatrix test [2012-12-23 Sun] o readIspyData: message instead of warning if NA in featureData [2012-12-24 Mon] o Added msnbase.r script [2012-12-24 Mon] CHANGES IN VERSION 1.7.11 ------------------------- o new 'pattern' argument to filterNA [2012-12-15 Sat] o vignette and man updates [2012-12-15 Sat] o filterNA(, pattern) tests [2012-12-15 Sat] CHANGES IN VERSION 1.7.10 ------------------------- o new droplevels.MSnSet S3 method [2012-12-14 Fri] o fixed errors in vignette and udpates [2012-12-14 Fri] o vignette build stops in case of error [2012-12-14 Fri] CHANGES IN VERSION 1.7.9 ------------------------ o Updating processing data on readIspyData [2012-12-05 Wed] o filterNA has a droplevels arg [2012-12-05 Wed] o featureCV's default cv.norm is 'sum' now [2012-12-11 Tue] o fixed featureCV for 1 sample [2012-12-11 Tue] CHANGES IN VERSION 1.7.8 ------------------------ o new featureCV function [2012-12-04 Tue] o more MSnSet combineFeatures tests [2012-12-04 Tue] o new TMT6 impurity matrix and fixed purityCorrect [2012-12-05 Wed] o combineFeatures now automatically computes feature CVs (using featureCV) and collates this in featureData [2012-12-05 Wed] o new exprsToRatios method (moved from pRoloc) [2012-12-05 Wed] o initial implementation of impurity correction using Cramer's rule (see MSnbase:::cramer4) [2012-12-05 Wed] CHANGES IN VERSION 1.7.7 ------------------------ o added scale.mean and scale.median MSnSet normalisation method [2012-11-30 Fri] o improvements to readMSData [2012-11-30 Fri] o small updates to caching code, max level 2 [2012-11-30 Fri] o readMSdata test [2012-12-01 Sat] CHANGES IN VERSION 1.7.6 ------------------------ o Fixed bug in readIspyData, reported by Claire Mulvey [2012-11-27 Tue] CHANGES IN VERSION 1.7.5 ------------------------ o dropping levels in readIspySilacData [2012-11-06 Tue] o fixed plotNA [2012-11-09 Fri] CHANGES IN VERSION 1.7.4 ------------------------ o exporting log method [2012-11-02 Fri] o private readIspySilacData function [2012-11-05 Mon] o updating '['-MSnSet to log intial/final dims [2012-11-05 Mon] CHANGES IN VERSION 1.7.3 ------------------------ o updating readMzTabData to properly capture experiment description [2012-10-12 Fri] CHANGES IN VERSION 1.7.2 ------------------------ o fixed readMSData for MS1 [2012-10-08 Mon] CHANGES IN VERSION 1.7.1 ------------------------ o fixed vignettes [2012-10-02 Tue] CHANGES IN VERSION 1.7.0 ------------------------ o Version bump for next devel release [2012-10-01 Mon] CHANGES IN VERSION 1.5.25 ------------------------- o fixed bug when quantifying exp of length 1 (reported by Colin Archer), added test [2012-09-26 Wed] o fixed parallel default to FALSE [2012-09-26 Wed] CHANGES IN VERSION 1.5.24 ------------------------- o updated clean, removePeaks, combineFeatures, purityCorrect, trimMz, plot, MSnSet-class examples to not use readMSData [2012-09-25 Tue] o fixed clean,MSnExp-method [2012-09-25 Tue] o space in log message in extractPrecSpectra [2012-09-25 Tue] CHANGES IN VERSION 1.5.23 ------------------------- o updated quantify documentation [2012-09-24 Mon] o changed all foo.class functions to foo_class [2012-09-24 Mon] CHANGES IN VERSION 1.5.22 ------------------------- o setting parallel default to FALSE [2012-09-22 Sat] o enhanced parallel in DESCRIPTION and detectCores() passed to registerDoMC [2012-09-23 Sun] CHANGES IN VERSION 1.5.21 ------------------------- o removed registerDoMC no visible global function NOTE [2012-09-21 Fri] o fixed NOTE about xvarname which was a bug [2012-09-21 Fri] CHANGES IN VERSION 1.5.20 ------------------------- o an immediate warning is thrown is any(centroided(object)) in quantify.MSnExp [2012-09-15 Sat] o mzTab file and loading time is now recorded in processingData [2012-09-15 Sat] o temporarily dontrun'ing' the mzTab read/write examples as OLS is down (and breaks rols) (note: modifed Rd files, not roxygen template) [2012-09-15 Sat] CHANGES IN VERSION 1.5.19 ------------------------- o updated all ReporterIons rda data [2012-09-13 Thu] o Using && in testing parallel, require(foreach and doMC) [2012-09-14 Fri] CHANGES IN VERSION 1.5.18 ------------------------- o new log method for MSnSet instances [2012-09-13 Thu] o new MAplot methods using generic and ma.plot/mva.pairs from affy [2012-09-13 Thu] CHANGES IN VERSION 1.5.17 ------------------------- o changed TMT7[7] mass from 229.26 to 230.17 and ReporterIons descriptions [2012-09-12 Wed] CHANGES IN VERSION 1.5.16 ------------------------- o parallel quantify is now always set to FALSE on Windows, fixing example checking issues [2012-09-11 Tue] o fixed types in plotMzDelta man [2012-09-11 Tue] CHANGES IN VERSION 1.5.15 ------------------------- o updating code to ggplot2 v0.9.2 [2012-09-07 Fri] CHANGES IN VERSION 1.5.14 ------------------------- o added platform test to use doMC (d.tenenbaum) [2012-08-31 Fri] CHANGES IN VERSION 1.5.13 ------------------------- o updated fillUp function [2012-08-15 Wed] o added tikzDevice to suggests [2012-08-16 Thu] o 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 ------------------------- o using knitr instead of pgfSweave and misc vignette updated[2012-08-13 Mon] o spectrum2 reporter plotting params updates [2012-08-14 Tue] o added reporterNames to NAMESPACE [2012-08-14 Tue] CHANGES IN VERSION 1.5.11 ------------------------- o type in filterNA log messaging and also rounding pNA [2012-06-07 Thu] o typo in demo vignette - Gb instead of Mb [2012-07-15 Sun] CHANGES IN VERSION 1.5.10 ------------------------- o Fixed readMSData instrumentInfo handling (reported by Gopuraja Dharmalingam) [2012-06-05 Tue] o new multiple file loading test in test_io [2012-06-05 Tue] CHANGES IN VERSION 1.5.9 ------------------------- o topN now properly updates processingData [2012-06-01 Fri] o combineFeatures updates featureNames based on the groupBy argument - updated demo vignette and man accordinlgy [2012-06-01 Fri] o additional parameters were not passed when normalise using vsn [2012-06-01 Fri] CHANGES IN VERSION 1.5.8 ------------------------- o added aa data in environment data.frame [2012-05-22 Tue] o fixed MSnbase:::subsetBy (used by topN) when ncol(object) == 1 [2012-05-25 Fri] o new nQuants function [2012-05-31 Thu] o minor vignettes updates [2012-05-31 Thu] o nQuants now return a matrix with col names, taken form sampleNames(object) [2012-05-31 Thu] CHANGES IN VERSION 1.5.7 ------------------------- o changed title method to exptitle to avoid conflict/confusion with graphics::title and consitency with expinfo method [2012-05-15 Tue] o changed email to expemail [2012-05-15 Tue] o Added rols to Suggests [2012-05-15 Tue] CHANGES IN VERSION 1.5.6 ------------------------- o new ionSource, analyser, detectorType, title accessor methods for MIAPE, pSet and MSnSet classes [2012-05-06 Sun] o updated quantify example to use data(itraqdata) instead of reading dummyiTRAQ.mzXML [2012-05-09 Wed] o initial mzTab write support [2012-05-10 Thu] o mzTab read support [2012-05-10 Thu] o updated demo and io vignettes with mzTab info [2012-05-10 Thu] CHANGES IN VERSION 1.5.5 ------------------------- o added email slot in MIAPE and accessor [2012-05-04 Fri] o added expinfo methods to pSet and MSnSet [2012-05-04 Fri] o updated itraqdata [2012-05-04 Fri] o misc man typos fixed [2012-05-04 Fri] o quantify now properly propagates processingData [2012-05-04 Fri] CHANGES IN VERSION 1.5.4 ------------------------- o automatically populating experiment data instrument info while reading data [2012-04-30 Mon] o msInfo fixed and exported [2012-04-30 Mon] o update demo vignette with 14 fractions analysis paragraph [2012-05-01 Tue] CHANGES IN VERSION 1.5.3 ------------------------- o extractSpectra is now defunct [2012-04-20 Fri] o 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] o 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] o Setting processingData in MSnSet initialisation. [2012-04-20 Fri] o Dropping index column from header. [2012-04-20 Fri] o new Spectrum class v0.2.0 has tic slot. [2012-04-21 Sat] o *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] o fixed normalisation boxplot titles and other tic/ionCount changes in demo vignette. [2012-04-21 Sat] o removed qual subetting in MSnSet's "[" method [2012-04-24 Tue] CHANGES IN VERSION 1.5.2 ------------------------- o transposing and MSnSet does _silently_ drop the protocolData now [2012-04-03 Tue] o fixed MSnExp pData creation for multiple files, feature names have a .fileNumber extension now. [2012-04-19 Thu] o testing for uniqueness of files (filenames) in readMSData [2012-04-19 Thu] o updated itraqdata.RData [2012-04-19 Thu] o added a paralle argument to quantify and using paralle = FALSE in vignette, to avoid duplicated display of the command [2012-04-19 Thu] o defined "reporterNames<-" generics [2012-04-19 Thu] o 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 ------------------------- o updated NA warning message in readIspyData [2012-03-05 Mon] o fixed combineFeatures/combineMatrixFeatures for 1 sample [2012-03-20 Tue] o image method for MSnSet instances [2012-03-20 Tue] o fixed bug in plotNA (first t was wring) [2012-03-21 Wed] o import plot from stats4 [2012-03-21 Wed] o using reshape2 [2012-03-30 Fri] CHANGES IN VERSION 1.5.0 ------------------------- o new devel version bump CHANGES IN VERSION 1.3.15 ------------------------- o new updateFeatureNames function [2012-02-17 Fri] o updated vignettes to illustrate vertical/horizontal combine [2012-02-17 Fri] o typo in normalised.Rd [2012-02-19 Sun] o TODO combine unit tests CHANGES IN VERSION 1.3.14 ------------------------- o new is.na.MSnSet [2012-02-16 Thu] o updated vignette and NA related man pages with cross-links [2012-02-16 Thu] CHANGES IN VERSION 1.3.13 ------------------------- o new plotNA method + doc [2012-02-15 Wed] o new filterNA method + doc + tests [2012-02-15 Wed] o added a check on 'n' in topN [2012-02-16 Thu] o created a .Rinstignore [2012-02-16 Thu] o Update package Rd [2012-02-16 Thu] CHANGES IN VERSION 1.3.12 ------------------------- o new topN methods + doc + tests [2012-02-14 Tue] CHANGES IN VERSION 1.3.11 ------------------------- o changed explicit close(file) in writeMgf methods to on.exit(close(file)) [2012-02-12 Sun] o typo in vignette [2012-02-13 Mon] CHANGES IN VERSION 1.3.10 ------------------------- o type in writeMgfData man [2012-02-07 Tue] o updated TITLE in writeMgfData [2012-02-08 Wed] CHANGES IN VERSION 1.3.9 ------------------------- o updated demo vignette [2012-02-03 Fri] o sorting numeric subsets in "[" pSet, as unsorted numerical indexes fails [2012-02-03 Fri] o 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 ------------------------- o Modified trimMz warning to report acquisition number [2012-02-01 Wed] o add 'experimentData(object, value) <- ' method for signature eSet and MIAPE [2012-02-02 Thu] o combine methods for MIAPE instances [2012-02-02 Thu] o combine methods for MSnProcess instances [2012-02-02 Thu] o changed qual drop warning into message in combineFeatures, updated test_MSnSet accordingly [2012-02-02 Thu] o new updateFvarLabels and updateSampleNames function [2012-02-03 Fri] o combine method for MSnSets [2012-02-03 Fri] o Updated demo vignette figure 8 [2012-02-03 Fri] CHANGES IN VERSION 1.3.7 ------------------------- o Speeded up writeMgfData [2012-01-28 Sat] o fixes for ggplot2 0.9.0 o added import(grid) and import(reshape) [2012-01-30 Mon] o importFrom(plyr, ...) instead of only llply [2012-01-31 Tue] o loading reshape and grid in vignette [2012-01-31 Tue] o fixed chunk 21 (label = quantitation-plot) [2012-01-31 Tue] CHANGES IN VERSION 1.3.6 ------------------------- o Updated NoteAboutSpeedAndMemory since parallel processing has been added. [2011-12-18 Sun] o Added CITATION [2012-01-27 Fri] o Added information to header output: acquisition number and precursor intensity [2012-01-27 Fri] o Added a test in plot.Spectrum2 for empty dataframe [2012-01-27 Fri] o moved foreach, doMC to enhances [2012-01-27 Fri] CHANGES IN VERSION 1.3.5 ------------------------- o added a gc() before mzR::close(msdata)... seems to help with Rcpp and ref classes issue. [2011-12-09 Fri] o added a show parameter to getCacheEnv to define .cache should be printed out before being returned. [2011-12-09 Fri] o added cache unit test [2011-12-09 Fri] o readMzXMLData is now defunct and remove xcms from Imports [2011-12-16 Fri] CHANGES IN VERSION 1.3.4 ------------------------- o 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] o fixed another bug/typo in readMSData [2011-12-06 Tue] o now running extractSprectum example again [2011-12-06 Tue] o setting default cache to 0, as cache=1 introduces unstabel behavious... will investigate that [2011-12-06 Tue] CHANGES IN VERSION 1.3.3 ------------------------- o added parallel computation for MSnExp quantitation using foreach with llply(..., .parallel=TRUE) [2011-12-03 Sat] o TODO document above in quantify-methods.Rd o added foreach and doMC in Suggests [2011-12-03 Sat] o added Spectrum removePeaks and clean'ing in readMSData [2011-12-05 Mon] CHANGES IN VERSION 1.3.2 ------------------------- o \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] o typo in Author@R [2011-11-14 Mon] o modified utils.removePeaks and utils.clean to call sapply instead of IRanges:sapply [2011-12-01 Thu] CHANGES IN VERSION 1.3.1 ------------------------- o Herve added BioGenerics as a dependency and import statement in NAMESPACE [2011-11-29 Tue] CHANGES IN VERSION 1.3.0 ------------------------- o Version bump for Bioc 2.10 devel CHANGES IN VERSION 1.2.0 ------------------------- o Version bump for Bioc 2.9 release CHANGES IN VERSION 1.1.28 ------------------------- o added pgfSweave to Suggests [2011-10-23 Sun] CHANGES IN VERSION 1.1.27 ------------------------- o fixed bug in readIspyData [2011-10-07 Fri] o removed (unexported) ratio code [2011-10-12 Wed] o added processing description when MSnSet['ing [2011-10-12 Wed] o man typos corrected [2011-10-14 Fri] o changed readMzXMLData to readMSData in tests [2011-10-14 Fri] o expecting warning for readMzXMLData in test_io [2011-10-14 Fri] CHANGES IN VERSION 1.1.26 ------------------------- o extractSpectra deprecated [2011-10-05 Wed] o small changes in cache.R functions [2011-10-05 Wed] o changed [, extractSpectra and extractPrecSpectra to update the .cache slot [2011-10-05 Wed] o MSnExp show method uses .cache when level==1. [2011-10-05 Wed] o 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 ------------------------- o added .cache slot to pSet class [2011-10-03 Mon] o added pSet initialize method to set .cache and .cache$level as '0'. [2011-10-03 Mon] o Check that level is defined in .cache and env is locked in pSet validity method. [2011-10-03 Mon] o updated itraqdata.RData [2011-10-03 Mon] o Deprecated readMzXMLData, added defunct.Rd [2011-10-03 Mon] o changed readMzXMLData to readMSData in man [2011-10-03 Mon] o updated show MSnExp for speed [2011-10-03 Mon] o updated read*Data is support cache = [0|1]. [2011-10-03 Mon] o updated precScanNum to use sapply(spectra(...), precScanNum) instead of unlist(eapply(assayData(...), precScanNum)) to preserve splectra order. [2011-10-03 Mon] o new cache.R file with @.cache related code [2011-10-03 Mon] CHANGES IN VERSION 1.1.24 ------------------------- o in readMgfData, SCANS is not used to populate acquisitionNum anymore, as several scans might have been combined upstreams [2011-09-26 Mon] o added fillUp function in utils.R and exported [2011-09-27 Tue] o new MSnbase-io vignette [2011-09-28 Wed] CHANGES IN VERSION 1.1.23 ------------------------- o fixed writeMgfData("MSnExp") [2011-09-21 Wed] o readMgfData now works when mz and intensty are separated by a '\t' (as exported by PRIDE Inspector) [2011-09-21 Wed] o show("MSnExp") now works without retention time [2011-09-21 Wed] o updated mgf2Spectrum2 to make it faster [2011-09-21 Wed] o fixed missing fromFile slot in data created from readMgfData that prevented calling header [2011-09-21 Wed] o readMgfData now creates a fData based on the peak header [2011-09-21 Wed] o modified getCurveWidth to work with centroided data [2011-09-21 Wed] o fixed bug getCurveWidth [2011-09-21 Wed] CHANGES IN VERSION 1.1.22 ------------------------- o removed (internal) Mascot query link column in readIspyData to work with latest ouput version [2011-09-12 Mon] o removed the fillUp part in readIspyData [2011-09-14 Wed] o exported readIspyData [2011-09-20 Tue] o removed link to proteomics sig list [2011-09-20 Tue] o removed url in DESCRIPTION [2011-09-20 Tue] o 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 OBJECTS! [2011-09-20 Tue] CHANGES IN VERSION 1.1.21 ------------------------- o updated write.exprs to add fData columns [2011-09-08 Thu] o added write.exprs and readMSnSet unit test [2011-09-08 Thu] CHANGES IN VERSION 1.1.20 ------------------------- o added a readMSnSet function [2011-09-08 Thu] o added a write.MSnSet("MSnSet") method [2011-09-08 Thu] o vignette/man updates - mainly data import section documenting readMSData and readMgfData [2011-09-08 Thu] ------------------------- o incorporating mzR io frame work [2011-09-05 Mon] o use mzR's peaksCount and header generics [2011-09-05 Mon] o added test to check that readMzXMLData and readMSData give same output [2011-09-05 Mon] o added readMSData.Rd doc file [2011-09-05 Mon] o added Author@R field in DESCRIPTION [2011-09-07 Wed] o compressed/resaved (using resaveRdaFiles) itraqdata.RData file to [2011-09-07 Wed] CHANGES IN VERSION 1.1.18 ------------------------- o read support for mgf files contributed by Guangchuang Yu [2011-07-06 Wed] o added as.ExpressionSet.MSnSet and setAs methods and updated MSnSet doc [2011-07-09 Sat] o fixed read/write mgf compatibility [2011-09-01 Thu] o added mgf io test [2011-09-01 Thu] o exported and document mfg read/write support [2011-09-01 Thu] o added centroided parameter to rawToSpectrum[1|2] to set this directly at object creation in readMzXmlData [2011-09-01 Thu] o other minor changes in Rd files [2011-09-01 Thu] o added warning checks for combineFeatures when verbose=TRUE in test_MSnSet.R [2011-09-02 Fri] CHANGES IN VERSION 1.1.17 ------------------------- o updated itraqdata manual [2011-06-27 Mon] o fixed bug in MSnSet validity method - msg was initialised to NULL when testing Biobase:::isValidVersion and Biobase::assayDataValidMembers [2011-07-02 Sat] o added t.MSnSet method [2011-07-02 Sat] o document t.MSnSet method [2011-07-05 Tue] o test for t-MSnSet [2011-07-05 Tue] o new "["-MSnSet method to properly subset qual slot [2011-07-06 Wed] o updated MSnSet validity method to check qual dims [2011-07-06 Wed] o combineFeatures now drops the spectrum-specific qual slot [2011-07-06 Wed] o test for "["-MSnSet [2011-07-06 Wed] CHANGES IN VERSION 1.1.16 ------------------------- o added addVigs2WinMenu call in .onAttach [2011-06-26 Sun] o added plotMzDelta paragraph in vignette [2011-06-26 Sun] CHANGES IN VERSION 1.1.15 ------------------------- o new names and description methods for ReporterIons [2011-06-16 Thu] o added validObject() checks [2011-06-16 Thu] o new removeReporters method [2011-06-16 Thu] o plotMzDelta is exported and documented [2011-06-17 Fri] CHANGES IN VERSION 1.1.14 ------------------------- o Adding plotMzDelta QC plot (not yet exported), contributed by Guangchuang Yu [2011-06-14 Tue] o created a locked environment to store amino.acids dataframe [2011-06-14 Tue] o 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 ------------------------- o changed pSet [[ method [2011-06-13 Mon] o additional updates pSet [[ method [2011-06-13 Mon] o added MSnExp subsetting error tests [2011-06-13 Mon] o 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 ------------------------- o added invisible(NULL) to all show methods [2011-06-08 Wed] o added centroided argument to plot.MSnExp [2011-06-09 Thu] CHANGES IN VERSION 1.1.11 ------------------------- o harmonised MSnExp and Spectrum plot axes labels [2011-05-18 Wed] o Added plotting customisation section in vignette [2011-05-18 Wed] o updated signature of plot2d method to "MSnExp" only [2011-05-18 Wed] o added/exported plotDensity methods [2011-05-18 Wed] o started QC vignette section [2011-05-18 Wed] o added preprocSelection and preprocSelectionTable functions [2011-05-18 Wed] o TODO document preprocSelection[Table] in vignette o reduces plot2d-figure and plotDensity-figure sizes using png [2011-05-19 Thu] o added plotDensity doc [2011-05-19 Thu] o added round param to preprocSelection[Table] [2011-05-19 Thu] o preprocSelection[Table] documented and exported [2011-05-19 Thu] o fixed bug in plot.Spectrum1 [2011-05-24 Tue] o changed removePeaks setGeneric explicit signature [2011-05-26 Thu] o added MassSpectrometry biocView [2011-05-27 Fri] CHANGES IN VERSION 1.1.10 ------------------------- o minor updates in demo vignette [2011-05-13 Fri] o added plot argument to plot methods [2011-05-16 Mon] o fix in makeImpuritiesMatrix [2011-05-16 Mon] o added meanSdPlot MSnSet method [2011-05-17 Tue] o minor cosmetic fix in purityCorrect error message [2011-05-17 Tue] o added method="sum" to Spectrum/MSnExp normalisation [2011-05-17 Tue] o typo in MSnSet-class.Rd corrected [2011-05-17 Tue] CHANGES IN VERSION 1.1.9 ------------------------- o exporting normali[s|z]e methods for MSnSet, Spectrum and MSnExp [2011-05-12 Thu] o added quantile normalisation [2011-05-12 Thu] o added quantile.robust normalisation [2011-05-12 Thu] o added vsn2 normalisation [2011-05-12 Thu] o added normalise manual [2011-05-12 Thu] o included normalisation section in vignette [2011-05-13 Fri] o more vignette updates [2011-05-13 Fri] o updated plotting methods to round MZ in title [2011-05-13 Fri] CHANGES IN VERSION 1.1.8 ------------------------- o added writeMgfData method from spectra and experiment [2011-05-09 Mon] o added writeMgfData manual [2011-05-09 Mon] o added itraqdata data set and updated vignette to use it [2011-05-11 Wed] o updated man pages to use tiny dummyiTRAQ.mzXML [2011-05-11 Wed] o added makeImpuritiesMatrix function [2011-05-11 Wed] CHANGES IN VERSION 1.1.7 ------------------------- o reporter ions purity correction method, man and test [2011-05-09 Mon] o updated vignette [2011-05-09 Mon] CHANGES IN VERSION 1.1.6 ------------------------- o added incomplete dissociation and spectral counting sections to demo vignette [2011-05-06 Fri] o added bioc-sig-proteomics link to foreword [2011-05-06 Fri] o type in foreword [2011-05-06 Fri] CHANGES IN VERSION 1.1.5 ------------------------- o added combineFeatures example in demo vignette [2011-05-05 Thu] CHANGES IN VERSION 1.1.4 ------------------------- o readIspyData updated to return updated factors [2011-05-03 Tue] o added unexported/undocumented combineFeatures function for MSnSets [2011-05-03 Tue] o added basic tests for combineFeatures [2011-05-03 Tue] o added combineFeatures manual [2011-05-04 Wed] o exportig combineFeatures [2011-05-04 Wed] CHANGES IN VERSION 1.1.3 ------------------------- o as.data.frame.Spectrum columns now are (first) mz and (second) intensity [2011-04-27 Wed] o exporting as.data.frame.Spectrum and coerce [2011-04-27 Wed] CHANGES IN VERSION 1.1.2 ------------------------- o Simplified quantify generic signature - now only object argument [2011-04-19 Tue] o Added strict parameter to quantify method, man updated, added relevant test o Added illustrative plot for quantitation methods in MSnbase-demo vignette [2011-04-19 Tue] o Added illustrative plot for data pre-processing (removePeaks and clean) in MSnbase-demo vignette [2011-04-20 Wed] o 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] o No warnings are issued anymore when reporter peaks are missing. See ?quantify on how to check this manually. [2011-04-20 Wed] o 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 ------------------------- o added setAs data.frame and as.data.frame methods for Spectrum objects [2011-03-29 Tue] o support for uncentroided MS2 spectra plots [2011-03-31 Thu] [2011-04-02 Sat] o support for uncentroided MS1 spectra plots [2011-04-02 Sat] o minor modification to readIspyData [2011-04-04 Mon] o removed centroided slot from MSnProcess and added to individial Spectrum instances. Relevant for Velos HCD (profile)/CID (uncentroided) data [2011-04-04 Mon] o modified readMzXmlData accordingly [2011-04-04 Mon] o added validObject(new(...)) tests for each class [2011-04-04 Mon] o added centroided[<-] methods to Spectrum and pSet [2011-04-04 Mon] o added 'keepAll' parameter to readIspyData [2011-04-11 Mon] CHANGES IN VERSION 0.99.4 ------------------------- o removed pgfSweave from Suggests field [2011-04-04 Mon] CHANGES IN VERSION 0.99.3 ------------------------- o Using Sweave rather than pgfSweave to build on lamb1. [2011-03-28 Mon] CHANGES IN VERSION 0.99.2 ------------------------- o updated references in package Rd [2011-03-24 Thu] o added readIspyData.Rd [2011-03-24 Thu] o removed old readMzXMLData function [2011-03-24 Thu] o cleaning up code [2011-03-24 Thu] o fixed MSnSet initialize: setting experimentData as MIAPE [2011-03-25 Fri] o fixed MSnSet initialize: identical featureNames in assayData and featureData for empty MSnExp istances [2011-03-25 Fri] o better test organisation and added object validity tests [2011-03-25 Fri] o updated readIspyData function [2011-03-25 Fri] CHANGES IN VERSION 0.99.1 ------------------------- o fake vignettes are copied back in inst/doc/. to make sur tar tarball can be extracted and build again [2011-03-24 Thu] o Making clean after make all [2011-03-24 Thu] CHANGES IN VERSION 0.99.0 ------------------------- o MSnProcess@process get's one line when subsetting and MSnExp object [2011-03-21 Mon] o Updated vignette Makefile [2011-03-22 Tue] o Added fake vignettes [2011-03-22 Tue] o Version set to 0.99.0 [2011-03-22 Tue] o Minor changes in quantify-method.Rd [2011-03-22 Tue] o added .Rbuildignore to ignore 'sweave-cache.*' [2011-03-22 Tue] o added R/zzz.R with start-up message [2011-03-23 Wed] o Added width generic [2011-03-23 Wed] o IRanges in now imported [2011-03-23 Wed] CHANGES IN VERSION 0.2.0 [2011-03-17 Thu] ------------------------ o MSnSet now extends eSet, reimplementing the ExpressionSet class with exception of the experimentData slot, that must now be a MIAPE instance. o updated MIAPE substantially and added accessor methods. o updated docs and vignettes to reflect above changes. CHANGES IN VERSION 0.1.5 ------------------------ o added zoo to Suggest, as zoo::rollapply is used in vignette. o 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). o added vns to Suggests, as it is used in the demo vignette. CHANGES IN VERSION 0.1.4 ------------------------ o added pgfSweave to Suggests, as is called in vignette Makefile CHANGES IN VERSION 0.1.3 ------------------------ o Updates to ReporterIons man page o Moved some Depends to Imports and updated NAMESPACE o corrected a IRanges:::sapply ot IRanges::sapply in utils.R o added inst/tests/test_MSnProcess.R CHANGES IN VERSION 0.1.2 ------------------------ o MSnProcess@MSnbaseVersion is not set in the initialize method instead to the prototype o changed R CMD to $(R_HOME)/bin/R CMD in inst/doc/Makefile o removed first and last (was 5th) MS1 spectra and associated MS2 spectra from dummy file to reduce size below 2MB. o Updated tests to reflect new dummy data set o Edition of dummy brakes readMzXMLData with msLevel=1 -- comment related tests o Updated MSnbase-demo vignette and man to use good spectra un plots (i.e "X43" instead of "X64") CHANGES IN VERSION 0.1.1 ------------------------ o Added LazyLoad: yes in DESCRIPTION and modified docs accordingly o Added NEWS file CHANGES IN VERSION 0.1.0 ------------------------ o Added MSnbase-demo vignette o Added MSnbase-development vignette