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