CHANGES IN VERSION 1.1.5 ------------------------ o updated references <2013-03-22 Fri> CHANGES IN VERSION 1.1.4 ------------------------ o added citation <2013-03-21 Thu> o vignette uses knitr engine and scrartcl class <2013-03-21 Thu> CHANGES IN VERSION 1.1.3 ------------------------ o knitr 1.0 compatibility, based on Dan's updates <2013-01-15 Tue> CHANGES IN VERSION 1.1.2 ------------------------ o added note about tcl BWidget package in synapterGUI man <2012-10-04 Thu> CHANGES IN VERSION 1.1.1 ------------------------ o fixing vignette <2012-10-02 Tue> CHANGES IN VERSION 1.1.0 ------------------------ o new devel version bump <2012-10-01 Mon> CHANGES IN VERSION 0.99.15 -------------------------- o updated ref in package man (2) <2012-09-14 Fri> o updated Synapter show method to display short log <2012-09-14 Fri> CHANGES IN VERSION 0.99.14 -------------------------- o updated ref in package man <2012-09-11 Tue> CHANGES IN VERSION 0.99.13 -------------------------- o bumping version number to take all previous changes into account <2012-08-29 Wed> CHANGES IN VERSION 0.99.12 -------------------------- o fixed build problem on windows <2012-08-27 Mon> o updated refs in vignette <2012-08-28 Tue> CHANGES IN VERSION 0.99.11 -------------------------- o using dev='pdf' in vignette and removing tikzDevice (not on CRAN anymore) from Suggests<2012-08-16 Thu> CHANGES IN VERSION 0.99.10 -------------------------- o added tikzDevice suggestion for vignette <2012-08-15 Wed> CHANGES IN VERSION 0.99.9 ------------------------- o using knitr instead of pgfSweave <2012-08-13 Mon> o new verbose arg to loadIdentOnly taken into account by estimateMasterFdr and makeMaster <2012-08-13 Mon> CHANGES IN VERSION 0.99.8 ------------------------- o vignette update with summary table <2012-07-17 Tue> o vignette update with additional PLGS slides <2012-07-17 Tue> CHANGES IN VERSION 0.99.7 ------------------------- o updated vignette <2012-07-12 Thu> o removed README.org file <2012-07-12 Thu> o added github page in DESCRIPTION <2012-07-12 Thu> CHANGES IN VERSION 0.99.6 ------------------------- o Masterpeptides has new fdr and method slots <2012-07-10 Tue> o added method arg to makeMaster <2012-07-10 Tue> o fixed non-match precuror.leIDs when using master <2012-07-11 Wed> CHANGES IN VERSION 0.99.5 ------------------------- o removed 'precursor.Mobility' columns from light merged and matched csv output, as these are not available when a MSe master is used <2012-07-09 Mon> CHANGES IN VERSION 0.99.4 ------------------------- o use log2 for t.test <2012-07-05 Thu> o updates to vignette <2012-07-06 Fri> CHANGES IN VERSION 0.99.3 ------------------------- o git/svn integration messing up and testing <2012-07-03 Tue> o late night testing <2012-07-03 Tue> CHANGES IN VERSION 0.99.2 ------------------------- o changed merged to total FDR in MasterFdrResults plot x label, as in manuscript <2012-06-13 Wed> o mention multtest in vignette <2012-06-13 Wed> o qvalue refs <2012-06-14 Thu> o Synapter.Rd updates, to match manuscript nomenclature <2012-06-14 Thu> o Added 'Getting help' section in vignette and package man page <2012-06-14 Thu> o Changed HDMSe to ident in plotGrid plot legend <2012-06-25 Mon> CHANGES IN VERSION 0.99.1 ------------------------- o Latex typo in vignette <2012-06-11 Mon> o Dan's suggestions for <2012-06-13 Wed> CHANGES IN VERSION 0.99.0 ------------------------- o bump version for Bioconductor submission <2012-06-08 Fri> CHANGES IN VERSION 0.9.1 ------------------------- o more doc completion <2012-06-07 Thu> o fixed type in dim <2012-06-07 Thu> o added PLGS ref and screenshots to vignette <2012-06-07 Thu> o finished methods documentation in Synapter.Rd <2012-06-07 Thu> o reduced screenshots sizes to get below 2M <2012-06-08 Fri> o fixed synapterGUI bug introduced during naming refactoring <2012-06-08 Fri> CHANGES IN VERSION 0.9.0 ------------------------- o moved repo to github <2012-06-06 Wed> o changed HDMSe/MSe naming convention to identification/quantitation <2012-06-06 Wed> o second round of naming changes (utils) <2012-06-07 Thu> o Description of package and methodology updated and references <2012-06-07 Thu> CHANGES IN VERSION 0.8.14 ------------------------- o Updated package title <2012-06-05 Tue> o removed PLGS vignette <2012-06-06 Wed> CHANGES IN VERSION 0.8.13 ------------------------- o more vignette work <2012-06-01 Fri> o added pgfSweave and xtable to Suggests and loaded in vignette <2012-06-01 Fri> CHANGES IN VERSION 0.8.12 ------------------------- o updated show MasterPeptides to reflect number of files effectively used <2012-05-28 Mon> o moved MasterFdrResults to S4 framework <2012-05-30 Wed> o MSnbase is now a dependency <2012-05-30 Wed> o vignette updates <2012-05-30 Wed> o synergise now calls filterUniqueDbPeptides even if master, as opposed to filterUniqueMSeDbPeptides <2012-05-30 Wed> o fixes as(, "MSnSet") - peptides sequences are now properly made unique <2012-05-30 Wed> CHANGES IN VERSION 0.8.11 ------------------------- o Automatic handling of Masterpeptides objects <2012-05-23 Wed> o Various man updated to describe the above <2012-05-23 Wed> o Now adding vignettes to windows vignette menu <2012-05-23 Wed> o fixed/improved writeMasterPeptides and fixed [tk_]choose.dir in synergise <2012-05-23 Wed> o MasterPeptides must be save as 'rds' with saveRDS to be reusable in synergise/Synapter <2012-05-23 Wed> CHANGES IN VERSION 0.8.10 ------------------------- o updated master-related function names by removing explicit reference to HDMSe <2012-05-16 Wed> o new AllGenerics.R and AllClasses.R files <2012-05-16 Wed> o removed selection param to makeMaster <2012-05-16 Wed> o new makeMaster returns an instance of class 'MasterPeptides' <2012-05-16 Wed> CHANGES IN VERSION 0.8.9 ------------------------ o new synergise verbose parameter <2012-05-11 Fri> o filterUnique[HDMSe|MSe]DbPeptides new verbose param <2012-05-11 Fri> o started method documentation in Synapter.Rd <2012-05-11 Fri> o import Vennerable::Venn <2012-05-15 Tue> o updated makeMasterHDMSe file - now has a 'selection' parameter, fixes issue #27. <2012-05-15 Tue> CHANGES IN VERSION 0.8.8 ------------------------ o man/vignette updates <2012-05-02 Wed> o added PLGS data input to vignette, contributed by Pavel <2012-05-02 Wed> o added Pavel's PLGS_Data_Processing.pdf slides as vignette <2012-05-03 Thu> o added Biobase import to benefit of addVigs2WinMenu <2012-05-03 Thu> o new plgsGuide() function to access the PLGS_Data_Processing vignette <2012-05-03 Thu> o fixed gui ppm.by label (issue #25) <2012-05-03 Thu> o License is GPL-2 <2012-05-03 Thu> o vignette improvements <2012-05-03 Thu> CHANGES IN VERSION 0.8.7 ------------------------ o added Nick's email to vignette <2012-04-30 Mon> o worked on gui - tree widget now expands when resizing window <2012-04-30 Mon> o added makeMasterHDMSe and estimateMasterFdr cross references <2012-05-01 Tue> o continued vignette <2012-05-01 Tue> o added synapterTiny test data <2012-05-01 Tue> o synapterTinyData to load and initialise the test data <2012-05-01 Tue> o synapterGuide sortcut to open vignette <2012-05-01 Tue> o synergise example (notrun, though) <2012-05-01 Tue> CHANGES IN VERSION 0.8.6 ------------------------ o Testing if model exists before findEMRTs/searchGrid <2012-04-27 Fri> o added fdr method choice in synergise <2012-04-27 Fri> o synergise code updates and documentation <2012-04-27 Fri> o work on vignette and new bib file <2012-04-27 Fri> o added package documentation and updated start-up message <2012-04-27 Fri> o added utils in imports <2012-04-27 Fri> CHANGES IN VERSION 0.8.5 ------------------------ o merged filterUniqueDbPeptides and filterUniquePeptides into filterUniqueDbPeptides in the Synapter class interface (same for MSe/HDMSe specific methods). Both are still distinct at the RefClass level though. <2012-04-27 Fri> o TODO - maybe add fdr method choice in synergise - DONE v 0.8.6 CHANGES IN VERSION 0.8.4 ------------------------ o new inspectPeptideScores function <2012-04-26 Thu> o finished gui code - synapterGUI exported <2012-04-27 Fri> o tested synapterGUI until report generation <2012-04-27 Fri> o TODO - avoid loading fasta db twice in filterUniqueDbPeptides CHANGES IN VERSION 0.8.3 ------------------------ o fixes getIdStats - now stops if any NA are found <2012-04-25 Wed> CHANGES IN VERSION 0.8.2 ------------------------ o fixed typo in data.frame column name <2012-04-25 Wed> CHANGES IN VERSION 0.8.1 ------------------------ o new masterFdr function that computes merged FDR - still under construction <2012-04-06 Fri> o updated Synapter.Rd <2012-04-23 Mon> o Only considered *unique peptides* (sequences) to calculate the p-values. The .[HD]MSePeptideScores dataframes are also updated so that plotPepScores and getPepNumbers also use unique() peptides to visualise the scores. <2012-04-23 Mon> o estimateMasterFdr (was masterFdr) is functional <2012-04-24 Tue> o estimateMasterFdr output stored in MasterFdrRes S3 class <2012-04-24 Tue> o TODO Investigate NA p-values - DONE - bug fixed in v 0.8.3 CHANGES IN VERSION 0.8.0 ------------------------ o added separate add[HD]MSeIdStats method <2012-04-06 Fri> o added separate filterUnique[HD]MSeDbPeptides method <2012-04-06 Fri> o added separate filterUnique[HD]MSeSeq method <2012-04-06 Fri> o new makeMasterHDMSe function <2012-04-06 Fri> o new Master field in .Synapter class <2012-04-06 Fri> o new loadMasterData function <2012-04-06 Fri> o modifed plotFdr and plotPepScores if master <2012-04-06 Fri> o updated Synapter constructor for master <2012-04-06 Fri> o new setMaster method <2012-04-06 Fri> o renames filterUniqueDBpeptides to filterUniqueDbPeptides and added filterUnique[HD]MSeDbPeptides methods in interface <2012-04-06 Fri> o fixes getPepNumbers for master HDMSe <2012-04-06 Fri> CHANGES IN VERSION 0.7.8 ------------------------ o renamed plotQvalues to plotFdr <2012-04-05 Thu> o new getFdrStats method <2012-04-05 Thu> CHANGES IN VERSION 0.7.7 ------------------------ o non-unique matched features now get NAs except for the first column (Function) <2012-04-04 Wed> o changed FDR adjustment; it is now possible to choose between 'BH' (default), 'Bonferroni' and 'qval' - see issue #22 <2012-04-04 Wed> o updated plotQvalues accordingly <2012-04-04 Wed> o fix in setBestGridParams (== to %in%) to avoid warnings when different nrow for prctModel (x) and details (y) best grid params <2012-04-04 Wed> CHANGES IN VERSION 0.7.6 ------------------------ o default span set to 0.05 <2012-03-26 Mon> o fix in setBestGridParams <2012-03-27 Tue> CHANGES IN VERSION 0.7.5 ------------------------ o fixed bug in getBestGridParams when what != "auto" and mutliple solutions <2012-03-26 Mon> o type in Synapter.Rd <2012-03-26 Mon> o changed ppm and nsd defaults in searchGrid to reflect defaults in synergise and gui <2012-03-26 Mon> o new 'object' parameter in synergise <2012-03-26 Mon> o updated inputFiles accessor (names and order) <2012-03-26 Mon> o fixed bug in searchGrid when using 'n' <2012-03-26 Mon> CHANGES IN VERSION 0.7.4 ------------------------ o using "model" as default parameter selection method <2012-03-23 Fri> o new "auto" parameter selection model - uses "model" and if multiple pairs, uses best "details" if any of ppm/nsd match <2012-03-23 Fri> o remove parameter selection method in gui - using auto <2012-03-24 Sat> o update html report - provide ppm and nsd values selected from grid search and auto method <2012-03-24 Sat> o updates to Synapter.Rd <2012-03-25 Sun> CHANGES IN VERSION 0.7.3 ------------------------ o dropped synergize spelling; too annoying when autocompleting <2012-03-22 Thu> o when computing grid details, checking if x["1"] or x["-1"] are NA and replacing by 0 <2012-03-22 Thu> o fixed bug in detail grid <2012-03-22 Thu> o now setting best params in synergize <2012-03-23 Fri> CHANGES IN VERSION 0.7.2 ------------------------ o synergi[s/z]e continued <2012-03-21 Wed> o also create a grid based on grid details. This actually fixes a bug in getBestGridParams 'details' search <2012-03-21 Wed> o Removed filterUniquePeptides from loadData, forgot to do that in version 0.7.1 <2012-03-21 Wed> o finished synergi[s|z]e <2012-03-22 Thu> Changes IN VERSION 0.7.1 ------------------------ o synergi[s/z]e definition <2012-03-08 Thu> o GUI implementation <2012-03-10 Sat> o cleaned performance method <2012-03-20 Tue> o new filterUniquePeptides method that filter peptides that appear multiple times in the respective HDMSe/MSe input peptide files. Previously, this was done when data was loaded. Also updated synergise, example and doc. <2012-03-21 Wed> CHANGES IN VERSION 0.7.0 ------------------------ o using filtered HDMSePeptideData (was mfHDMSePeptideData) to do the matching; mf[HD]MSePeptideData have been dropped for Synapter class <2012-03-07 Wed> o new dims method <2012-03-07 Wed> o best grid parameter selection based on +1/(+1 + -1) proportion of correct unique identifications (issue #18) <2012-03-07 Wed> CHANGES IN VERSION 0.6.0 ------------------------ o fixed bug when providing filenames to Synapter <2012-03-06 Tue> o added 'n' parameter to searchGrid to specify a number of features to be used for the grid search <2012-03-06 Tue> o Test if n > nrow(HDMSe peptides), warn and use all HDMSe peptides <2012-03-06 Tue> o moved some parameter initialisation from searchGrid method to searchGrid interface <2012-03-06 Tue> o new filterUniqueDbPeptides method; this is NOT done anymore when the data is loaded <2012-03-06 Tue> CHANGES IN VERSION 0.5.3 ------------------------ o new write[HD]MSePeptides methods <2012-02-17 Fri> CHANGES IN VERSION 0.5.2 ------------------------ o added require(MSnbase) in setAs <2012-02-14 Tue> o removed pre/post-fix peptides - is not an issue <2012-02-14 Tue> CHANGES IN VERSION 0.5.1 ------------------------ o new setAs method to coerce a Synapter instance into an MSnSet object <2012-02-14 Tue> o added MSe prot FPR filter when calculating performance <2012-02-14 Tue> CHANGES IN VERSION 0.5.0 ------------------------ o filtering HDMSe unique peptides <2012-02-12 Sun> o added explicit values to be set for setPpmError and setRtNsd in Synapter man example <2012-02-13 Mon> o filtering pep score (q-val) AND prot FPR (NEW) before matching EMRTs and calculating performance <2012-02-13 Mon> o filtering HDMSe unique peptides <2012-02-13 Mon> o fasta file is also asked for when creating instance <2012-02-13 Mon> o Filtering unique (i.e. non duplicated peptide sequences) is now done when data is loaded, after db unique peptide filtering, to get rid of pre/post-fix cases (like ABCD and ABCDXXXX) that are not removed by filterUniqueDbPeptides/dbUniquePeptideSet. <2012-02-13 Mon> o keeping common HDMSe/MSe peptides filter is not included in merge Peptides (filterPepSeq removed) <2012-02-13 Mon> o removed (private) filter and idStats parameters <2012-02-13 Mon> o updated documentation <2012-02-13 Mon> o updated performace; removed duplicates count as there are no duplicated sequences/precursor.leIDs anymore <2012-02-13 Mon> o removing duplicated assigned EMRTs; these rows in the matched results dataframes are identified with a -1 <2012-02-13 Mon> o new getLog method <2012-02-14 Tue> o updaed show method <2012-02-14 Tue> Changes IN VERSION 0.4.7 ------------------------ o fixed 'performance' typo in Synapter man <2012-02-09 Thu> o fixed bug in performance/getBestGridValue (issues #5 and #6) <2012-02-10 Fri> o Updated performance method <2012-02-10 Fri> o Added p/q-values to 'light' merged output <2012-02-10 Fri> CHANGES IN VERSION 0.4.6 ------------------------ o HDMSePeptideData is updated (predictRt and sdRt columns) when rt is modelled. <2012-02-09 Thu> o Updated doHDMSePredictions to either predict rt using the model (as previously) or retrieve that data from the HDMSePeptideData data.frame (new). <2012-02-09 Thu> o doHDMSePredictions now returns a list. <2012-02-09 Thu> o added a subet parameter to searchGrid <2012-02-09 Thu> o added a performace method (see issue #1) <2012-02-09 Thu> CHANGES IN VERSION 0.4.5 ------------------------ o removed extra plotRtDiff un Synapter example <2012-02-07 Tue> o findMSeEMRTs tidy-up, added a matched.mse.spectrumIDs column to the MatchedEMRTs data.frame; this stores the MSePep3D spectrumIDs that were macthed within an ErrorPpm by RtNsd window. <2012-02-07 Tue> o added writeMergedPeptides/writeMatchedEMRTs file argument examples. <2012-02-07 Tue> o PpmError and RtNsd checked/set only for plotFeatures(, what = "some") and not what = "all" anymore. <2012-02-07 Tue> o Added the recursor.leID.mse column to the MatchedEMRTs data.frame with merged MSe IDs corresponding to the HDMSe IDs used for rt modelling <2012-02-07 Tue> o grd2 is now computed using new MatchedEMRTs columns <2012-02-07 Tue> o function to get assignment details <2012-02-08 Wed> o code clean-up: xx$HDMSePeptideData is now filtered for peptide score fdr explicitely by the top-level caller (in synapter-class), rather than (redundantely) inside findMSeEMRTs and in gridSearch2 (which also calls the latter). Removed fdr parameter in these functions as unused. This is also documented now. <2012-02-09 Thu> o code clean-up: remove old gridSearch call and definition <2012-02-09 Thu> CHANGES IN VERSION 0.4.4 ------------------------ o fixed writeMatchedEMRTs/writeMergedPeptides(..., what = "full") <2012-02-07 Tue> o Synapter constructor has filenames argument <2012-02-07 Tue> CHANGES IN VERSION 0.4.3 ------------------------ o continued documentation <2012-01-31 Tue> <2012-02-01 Wed> o added plotRtDiffs in example <2012-02-01 Wed> o added warning and nsd[1:3] selection in plotRt model <2012-02-01 Wed> o fixed bug in filterPepSeq; wring MSe dimensions where writton to log <2012-02-03 Fri> o new getEMRTtable method <2012-02-03 Fri> o added ... to plotRtDiffs to be passed to hist <2012-02-03 Fri> CHANGES IN VERSION 0.4.2 ------------------------ o Matched EMRTs dataframe cols class is set explicitly based on HDMSePeptideData and MSePep3DData cols classes <2012-01-30 Mon> o Grid search on percentage of correct assignments <2012-01-30 Mon> o updated grid getters/setters accordingly <2012-01-31 Tue> CHANGES IN VERSION 0.4.1 ------------------------ o added legend to plotFeature(..., what="some") <2012-01-27 Fri> o added protein false positive rate functionality <2012-01-27 Fri> CHANGES IN VERSION 0.4.0 ------------------------ o introducing ReferenceClasses implementation <2012-01-13 Fri> o filterPepScore takes medianRndScore and stdRndScore as separate parametres instead as a list (params) <2012-01-14 Sat> o fixed a typo in makeSynapterReport <2012-01-16 Mon> o changed several function parameters from input$... into ... <2012-01-17 Tue> o further changes to gridSearch, doHDMSePredictions and findMSeEMRTs to integrate with ref classes implementation <2012-01-17 Tue> o rationalised findMSeEMRTs and gridSearch 'sapply' loops <2012-01-17 Tue> o new keepUniqueSpectrumIds function, now called explicitely before gridSearch and findMSeEMRTs <2012-01-18 Wed> o Testing that changes produce same makeSynapterReport results than version 0.3.2 <2012-01-17 Tue> o added identification p/q-values calculation and qvalue and multtest in imports <2012-01-23 Mon> o global filtering is now done when data is loaded; can also be done manually <2012-01-23 Mon> o removing PLGS pepscore filtering and HDMSe log input <2012-01-24 Tue> o added qvalue and peptide score plots <2012-01-24 Tue> o Synapter ref class interface using S4 methods <2012-01-25 Wed> o Doing mass error filtering on the individual peptide files instead of merged data. <2012-01-26 Thu> o mf[HD]MSePeptideData is not initialised when files are loaded <2012-01-26 Thu> o Documentating new interface <2012-01-26 Thu> o added getRtQs and plotRtDiffs <2012-01-27 Fri> CHANGES IN VERSION 0.3.2 ------------------------ o save intermediate filtering tables <2011-12-23 Fri> o added ... to plotLowess2 <2012-01-09 Mon> CHANGES IN VERSION 0.3.1 ------------------------ o changed figures url to relative <2011-12-22 Thu> o added synapter version and date to report output <2011-12-22 Thu> o updated filter.error.ppm to specify column name to use as filter <2011-12-22 Thu> o new mass error plot <2011-12-22 Thu> o added orignal nrows in filtering summary table <2011-12-22 Thu> o when provided, htmldir is now created automatically <2011-12-22 Thu> CHANGES IN VERSION 0.3.0 ------------------------ o modified rt range calculation <2011-12-20 Tue> o modified feature plot to incorporate rt and mass ranges <2011-12-20 Tue> o adjusted lowess plots ylims to rt modelling range <2011-12-20 Tue> o saving light result tables <2011-12-21 Wed> o added option to perform grid search over ppm and nsd to maximise the number of unique matches <2011-12-21 Wed> o added full range feature plots <2011-12-21 Wed> CHANGES IN VERSION 0.2.0 ------------------------ o fixed bug when input was not called 'input' <2011-12-16 Fri> o can now set output directory in makeSynapterReport <2011-12-16 Fri> o using CairoSVG <2011-12-16 Fri> CHANGES IN VERSION 0.1.0 ------------------------ o initial release <2011-12-15 Thu>