CHANGES IN VERSION 1.13.1 ------------------------- o Update call to nQuants to accomodate changes in MSnbase (see commit #ce637b87e491a2f4c9f93490b2f4c7027cbfce16) <2016-02-29 Mon> o Defunct synapterGUI <2016-02-29 Mon> CHANGES IN VERSION 1.13.0 ------------------------- o Bioc devel 3.2 CHANGES IN VERSION 1.12.0 ------------------------- o Bioc release 3.1 CHANGES IN VERSION 1.11.2 ------------------------- o fixing bug introduced in 1.11.1 when coercing from Synapter to MSnSet object - see this post on the support forum for details https://support.bioconductor.org/p/71087/ <2015-09-27 Sun> CHANGES IN VERSION 1.11.1 ------------------------- o avoiding error when some fcols are missing when coercing from Synapter to MSnSet object - see this post on the support forum for details https://support.bioconductor.org/p/71087/ <2015-09-07 Mon> CHANGES IN VERSION 1.9.5 ------------------------ o update cross reference to qvalue::plot.qvalue in Synapter man page; closes #86 [2015-03-31 Tue] CHANGES IN VERSION 1.9.4 ------------------------ o use biocstyle [2015-01-23 Fri] o use requireNamespace [2015-01-23 Fri] CHANGES IN VERSION 1.9.3 ------------------------ o Filter entries in quantiation final peptides and Pep3D data that don't match in their intensity valus; see #42 for details. [2014-11-26 Wed] CHANGES IN VERSION 1.9.2 ------------------------ o Only suggesting tcltk and tcltk2, as gui is now deprecated [2014-11-21 Fri] CHANGES IN VERSION 1.9.1 ------------------------ o Deprecating synatperGUI [2014-11-10 Mon] o Directing questions to the Bioc support site [2014-11-10 Mon] CHANGES IN VERSION 1.9.0 ------------------------ o new devel version for Bioc 3.1 CHANGES IN VERSION 1.7.0 ------------------------ o Deprecating synatperGUI [2014-11-10 Mon] o Directing questions to the Bioc support site [2014-11-10 Mon] CHANGES IN VERSION 1.5.7 ------------------------ o Enable setting number of missed cleavages (closes #53) [2014-03-24 Mon] CHANGES IN VERSION 1.5.6 ------------------------ o change the default value of grid.ppm.from to 2 (was 5 before) [2014-03-05 Wed] o change the separator in GridDetails' names to ":" (was "." before) [2014-03-07 Fri] o test for corresponding Pep3D file (closes #42) [2014-03-19 Wed] CHANGES IN VERSION 1.5.5 ------------------------ o fix a bug in the calculation of non unique matches in gridSearch2 (part of searchGrid); results in a higher number of non unique matches (some of the reported -2 will now be reported as 2 in the grid details) [2014-03-05 Wed] o partial rewrite of gridSearch2 (part of searchGrid) for faster grid calculation [2014-03-04 Tue] CHANGES IN VERSION 1.5.4 ------------------------ o biocViews update CHANGES IN VERSION 1.5.3 ------------------------ o modified findMSeEMRTs (part of searchGrid) for faster grid calculation [2014-02-28 Fri] o typos in manual [2014-02-25 Tue] o replace readFasta by Biostrings::readAAStringSet [2014-02-25 Tue] o replace digest by cleaver::cleave [2014-02-25 Tue] CHANGES IN VERSION 1.5.1 ------------------------ o typo in vignette [2014-02-18 Tue] CHANGES IN VERSION 1.5.0 ------------------------ o new devel version for Bioc 2.14 CHANGES IN VERSION 1.3.4 ------------------------ o estimateMasterFdr now support list of vector as pepfiles [2013-09-27 Fri] o import(MSnbase) [2013-09-27 Fri] CHANGES IN VERSION 1.3.3 ------------------------ o Updated references. [2013-07-05 Fri] CHANGES IN VERSION 1.3.2 ------------------------ o fixed bug when using findEMRTs = "copy" [2013-05-30 Thu] CHANGES IN VERSION 1.3.1 ------------------------ o Reporting total number of peptides in dbUniquePeptideSet. Fixes issue #41. [2013-05-13 Mon] o New mergedEMRTs arg in findEMRTs. Closes issue #38. [2013-05-13 Mon] o fixed synapterTiny$QuantPep3DData, which had the rownames as first column synapterTiny$QuantPep3DData$X. Detected thanks to new mergedEMRTs arg. [2013-05-13 Mon] o added mergedEMRTs arg to synergise [2013-05-22 Wed] o Synapter checks that one file per list element is passed [2013-05-28 Tue] o minor typo/fixes [2013-05-28 Tue] o new idSource column when matching EMRTs [2013-05-29 Wed] o new performance2 method that shows identification source and NA values contingency table [2013-05-29 Wed] o new filterPeptideLength method [2013-05-29 Wed] o added peplen argument to synergise to filter on peptide length [2013-05-29 Wed] CHANGES IN VERSION 1.3.0 ------------------------ o Bioc 2.13 devel version bump CHANGES IN VERSION 1.2.0 ------------------------ o Bioc 2.12 stable version bump 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]