CHANGES IN VERSION 1.12.1 ------------------------- o updated readMSData test unit to ignore object@.__classVersion__ that fails with latest R/Bioc versions [2014-04-18 Fri] CHANGES IN VERSION 1.12.0 ------------------------- o Version bump for Bio 2.14 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