1. synapter
  2. NEWS.md
Raw Blame Patch Log History
# Synapter 2.21 ## Changes in version 2.21.1 - Render fragmentmatching.Rmd with rmarkdown::html_document() (see #139) # Synapter 2.17 ## Changes in version 2.17.3 - put commented code chunk back in ## Changes in version 2.17.2 - fix error in vignette ## Changes in version 2.17.1 - Update Laurent's email address # Synapter 2.5 ## Changes in version 2.5.2 - Use `BiocManager::install` [2018-07-16]. ## Changes in version 2.5.0 - New version for Bioconductor devel # Synapter 2.4 ## Changes in version 2.4.0 - New version for Bioconductor release # Synapter 2.3 ## Changes in version 2.3.1 - Partly revert 95f4094 because MSnbase:::utils.applyColumnwiseByGroup is gone. - Use `html_document` instead of `html_document2` in the vignettes [2018-01-17]. # Synapter 2.1 ## Changes in version 2.1.1 - Partly revert 95f4094 because MSnbase:::utils.applyColumnwiseByGroup is gone. # Synapter 2.0 - Version bump for Bioc release version 3.5. # Synapter 1.99 ## Changes in version 1.99.2 - update show,MasterPeptides to check of there's a fragmentlibrary slot before trying to access it <2017-04-19 Wed> ## Changes in version 1.99.1 - update NEWS file <2017-04-11 Tue> ## Changes in version 1.99.0 ### New features #### Ion mobility/Grid search. - Replace 2D grid search (retention time, *m/z*) of synapter1 by 3D grid search (retention time, *m/z*, ion mobility); set argument `imdiff = Inf` to get the original 2D grid search; closes [#33](https://github.com/lgatto/synapter/issues/33). - Add `{set,get}ImDiff` methods. - `getGrid` returns an array instead of a matrix (because of the new 3D grid search) [2014-05-16 Fri]. - `plotFeatures(..., what = "all")` gains a new argument: "ionmobilty" to plot *m/z* vs ionmobility as well. [2014-05-16 Fri] - `plotGrid` gets a new argument "maindim" to decided which of the three dimension should be used. [2014-05-16 Fri] - Add `filterNonUniqueIdentMatches` to remove matches of multiple identification data to a single quantitation entry (see [#111](https://github.com/lgatto/synapter/issues/111) for details) [2016-02-22 Mon]. #### Fragment matching - Load identification fragments (`final_fragments.csv`) and quantitation spectra (`Spectrum.xml`) via `Synapter` constructor. - New functions: `fragmentMatchingPerformance`, `filterUniqueMatches`, `filterNonUniqueMatches`, `filterFragments`, `plotCumulativeNumberOfFragments`, `plotFragmentMatchingPerformance`, `getIdentificationFragments` and `getQuantitationSpectra`. - Integrate a fragment library into *master* objects; closes [#63](https://github.com/lgatto/synapter/issues/63) and [#74](https://github.com/lgatto/synapter/issues/74). #### Misc - Allow to use an RDS instead of a fasta file as 'Unique Peptides Database', adds `createUniquePeptideDbRds`; closes [#55](https://github.com/lgatto/synapter/issues/55) [2014-04-29 Tue]. - Introduce `IisL` argument to `dbUniquePeptideSet` which treats I/L as same aminoacid if `IisL == TRUE` (default: `IisL = FALSE`); closes [#60](https://github.com/lgatto/synapter/issues/60) [2014-04-30 Wed]. - Add `rescueEMRTs` functions; replaces the argument `mergedEMRTs` in `findEMRTs`; closes [#93](https://github.com/lgatto/synapter/issues/93) [2015-07-26 Sun]. - Add `synergise2` which combines the integrates the new 3D grid search, the fragment matching; and uses slightly different default arguments than `synergise1`; closes [#119](https://github.com/lgatto/synapter/issues/119) [2016-10-25 Di]. - Load isotopic distributions from Pep3D data and also export them to MSnSet, to allow the correction of detector saturation; closes [#39](https://github.com/lgatto/synapter/issues/39) [2015-03-29 Sun]. - Add `synapterPlgsAgreement` to find agreement between *synapter* and *PLGS*; closes [#73](https://github.com/lgatto/synapter/issues/73). - Introduce `modelIntensity` to correct systematic intensity shifts (similar to `modelRt`); closes [#116](https://github.com/lgatto/synapter/issues/116). ### Improvements - Extract the ion that was used for identification (`isFid == 1`) from the Pep3D file instead of the first instance [2014-05-13 Tue]. - Add `updateObject` and `validObject` method [2014-11-16 Sun]. - Rename `QuantPep3DData$Function` column into `QuantPep3DData$matchedEMRTs`; closes [#67](https://github.com/lgatto/synapter/issues/67) [2015-07-26 Sun]. - Use just unique peptides in master creation (see [#107](https://github.com/lgatto/synapter/issues/107)) [2016-01-23 Sat]. - New `rmarkdown` based reports for `synergise1` (synonym to `synergise`) and `synergise2`. ### Bugfixes - Use new loess model in master creation (now based on m-estimator instead of least squares, identical to retention time model in classical synergise workflow; see [#107](https://github.com/lgatto/synapter/issues/107) for details) [2016-01-23 Sat] - Fix retention time model calculation in `plotFeatures(..., what="some")` [2014-04-28 Mon]. ### Internal changes - Add `testthat` to Suggests [2014-04-25 Fri]. - Add recommended biocView [2014-06-05 Thu]. - Replace `any(is.na(...)` by `anyNA(...)`; *synapter* depends on `R >= 3.1.0` now [2014-11-01 Sat]. - Add `ClassVersion` field to `Synapter` class [2014-11-21 Fri]. - Add `Versioned` class as parent class to `MasterPeptides` and `MasterFdrResults` [2014-11-22 Sat]. - Adapt `synergise` to new grid search (closes [#81](https://github.com/lgatto/synapter/issues/81)) [2016-10-16 So]. - Replace `hwriter` by `rmarkdown` report in `synergise`; closes [#120](https://github.com/lgatto/synapter/issues/120). [2016-10-17 Mon] ### Removed functions/arguments - Remove `synapterGUI`. - Remove unused internal functions: `filterCommonSeq`, `filterKeepUniqueSeq`, `filterKeepUniqueProt` [2014-11-27 Thu]. - Remove "mergedEMRTs" argument from `findEMRTs`. Now `rescueEMRTs` has to be called manually at the end of the processing; close [#93](https://github.com/lgatto/synapter/issues/93) [2015-07-26 Sun] - Remove "light" version of `writeMergedPeptides` and `writeMachtedPeptides` (now always the full `data.frame` is saved; see [#95](https://github.com/lgatto/synapter/issues/95)) [2016-10-16 Sun] - Update `synapterTiny` and `synapterTinyData` [2016-10-16 So] # Synapter 1.13 ## Changes in version 1.13.1 - Update call to nQuants to accomodate changes in MSnbase (see commit #ce637b87e491a2f4c9f93490b2f4c7027cbfce16) <2016-02-29 Mon> - Defunct synapterGUI <2016-02-29 Mon> ## Changes in version 1.13.0 - Bioc devel 3.2 # Synapter 1.12 ## Changes in version 1.12.0 - Bioc release 3.1 # Synapter 1.11 ## Changes in version 1.11.2 - 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 - 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> # Synapter 1.9 ## Changes in version 1.9.5 - update cross reference to qvalue::plot.qvalue in Synapter man page; closes [#86](https://github.com/lgatto/synapter/issues/86) [2015-03-31 Tue] ## Changes in version 1.9.4 - use biocstyle [2015-01-23 Fri] - use requireNamespace [2015-01-23 Fri] ## Changes in version 1.9.3 - Filter entries in quantiation final peptides and Pep3D data that don't match in their intensity valus; see [#42](https://github.com/lgatto/synapter/issues/42) for details. [2014-11-26 Wed] ## Changes in version 1.9.2 - Only suggesting tcltk and tcltk2, as gui is now deprecated [2014-11-21 Fri] ## Changes in version 1.9.1 - Deprecating synatperGUI [2014-11-10 Mon] - Directing questions to the Bioc support site [2014-11-10 Mon] ## Changes in version 1.9.0 - new devel version for Bioc 3.1 # Synapter 1.7 ## Changes in version 1.7.0 - Deprecating synatperGUI [2014-11-10 Mon] - Directing questions to the Bioc support site [2014-11-10 Mon] # Synapter 1.5 ## Changes in version 1.5.7 - Enable setting number of missed cleavages (closes [#53](https://github.com/lgatto/synapter/issues/53)) [2014-03-24 Mon] ## Changes in version 1.5.6 - change the default value of grid.ppm.from to 2 (was 5 before) [2014-03-05 Wed] - change the separator in GridDetails' names to ":" (was "." before) [2014-03-07 Fri] - test for corresponding Pep3D file (closes [#42](https://github.com/lgatto/synapter/issues/42)) [2014-03-19 Wed] ## Changes in version 1.5.5 - 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] - partial rewrite of gridSearch2 (part of searchGrid) for faster grid calculation [2014-03-04 Tue] ## Changes in version 1.5.4 - biocViews update ## Changes in version 1.5.3 - modified findMSeEMRTs (part of searchGrid) for faster grid calculation [2014-02-28 Fri] - typos in manual [2014-02-25 Tue] - replace readFasta by Biostrings::readAAStringSet [2014-02-25 Tue] - replace digest by cleaver::cleave [2014-02-25 Tue] ## Changes in version 1.5.1 - typo in vignette [2014-02-18 Tue] ## Changes in version 1.5.0 - new devel version for Bioc 2.14 # Synapter 1.3 ## Changes in version 1.3.4 - estimateMasterFdr now support list of vector as pepfiles [2013-09-27 Fri] - import(MSnbase) [2013-09-27 Fri] ## Changes in version 1.3.3 - Updated references. [2013-07-05 Fri] ## Changes in version 1.3.2 - fixed bug when using findEMRTs = "copy" [2013-05-30 Thu] ## Changes in version 1.3.1 - Reporting total number of peptides in dbUniquePeptideSet. Fixes issue [#41](https://github.com/lgatto/synapter/issues/41). [2013-05-13 Mon] - New mergedEMRTs arg in findEMRTs. Closes issue [#38](https://github.com/lgatto/synapter/issues/38). [2013-05-13 Mon] - fixed synapterTiny\$QuantPep3DData, which had the rownames as first column synapterTiny\$QuantPep3DData\$X. Detected thanks to new mergedEMRTs arg. [2013-05-13 Mon] - added mergedEMRTs arg to synergise [2013-05-22 Wed] - Synapter checks that one file per list element is passed [2013-05-28 Tue] - minor typo/fixes [2013-05-28 Tue] - new idSource column when matching EMRTs [2013-05-29 Wed] - new performance2 method that shows identification source and NA values contingency table [2013-05-29 Wed] - new filterPeptideLength method [2013-05-29 Wed] - added peplen argument to synergise to filter - n peptide length [2013-05-29 Wed] ## Changes in version 1.3.0 - Bioc 2.13 devel version bump # Synapter 1.2 ## Changes in version 1.2.0 - Bioc 2.12 stable version bump # Synapter 1.1 ## Changes in version 1.1.5 - updated references [2013-03-22 Fri] ## Changes in version 1.1.4 - added citation [2013-03-21 Thu] - vignette uses knitr engine and scrartcl class [2013-03-21 Thu] ## Changes in version 1.1.3 - knitr 1.0 compatibility, based on Dan's updates [2013-01-15 Tue] ## Changes in version 1.1.2 - added note about tcl BWidget package in synapterGUI man [2012-10-04 Thu] ## Changes in version 1.1.1 - fixing vignette [2012-10-02 Tue] ## Changes in version 1.1.0 - new devel version bump [2012-10-01 Mon] # Synapter 0.99 ## Changes in version 0.99.15 - updated ref in package man (2) [2012-09-14 Fri] - updated Synapter show method to display short log [2012-09-14 Fri] ## Changes in version 0.99.14 - updated ref in package man [2012-09-11 Tue] ## Changes in version 0.99.13 - bumping version number to take all previous changes into account [2012-08-29 Wed] ## Changes in version 0.99.12 - fixed build problem on windows [2012-08-27 Mon] - updated refs in vignette [2012-08-28 Tue] ## Changes in version 0.99.11 - using dev='pdf' in vignette and removing tikzDevice (not on CRAN anymore) from Suggests[2012-08-16 Thu] ## Changes in version 0.99.10 - added tikzDevice suggestion for vignette [2012-08-15 Wed] ## Changes in version 0.99.9 - using knitr instead of pgfSweave [2012-08-13 Mon] - new verbose arg to loadIdentOnly taken into account by estimateMasterFdr and makeMaster [2012-08-13 Mon] ## Changes in version 0.99.8 - vignette update with summary table [2012-07-17 Tue] - vignette update with additional PLGS slides [2012-07-17 Tue] ## Changes in version 0.99.7 - updated vignette [2012-07-12 Thu] - removed README.org file [2012-07-12 Thu] - added github page in DESCRIPTION [2012-07-12 Thu] ## Changes in version 0.99.6 - Masterpeptides has new fdr and method slots [2012-07-10 Tue] - added method arg to makeMaster [2012-07-10 Tue] - fixed non-match precuror.leIDs when using master [2012-07-11 Wed] ## Changes in version 0.99.5 - 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 - use log2 for t.test [2012-07-05 Thu] - updates to vignette [2012-07-06 Fri] ## Changes in version 0.99.3 - git/svn integration messing up and testing [2012-07-03 Tue] - late night testing [2012-07-03 Tue] ## Changes in version 0.99.2 - changed merged to total FDR in MasterFdrResults plot x label, as in manuscript [2012-06-13 Wed] - mention multtest in vignette [2012-06-13 Wed] - qvalue refs [2012-06-14 Thu] - Synapter.Rd updates, to match manuscript nomenclature [2012-06-14 Thu] - Added 'Getting help' section in vignette and package man page [2012-06-14 Thu] - Changed HDMSe to ident in plotGrid plot legend [2012-06-25 Mon] ## Changes in version 0.99.1 - Latex typo in vignette [2012-06-11 Mon] - Dan's suggestions for [2012-06-13 Wed] ## Changes in version 0.99.0 - bump version for Bioconductor submission [2012-06-08 Fri] ## Changes in version 0.9.1 - more doc completion [2012-06-07 Thu] - fixed type in dim [2012-06-07 Thu] - added PLGS ref and screenshots to vignette [2012-06-07 Thu] - finished methods documentation in Synapter.Rd [2012-06-07 Thu] - reduced screenshots sizes to get below 2M [2012-06-08 Fri] - fixed synapterGUI bug introduced during naming refactoring [2012-06-08 Fri] ## Changes in version 0.9.0 - moved repo to github [2012-06-06 Wed] - changed HDMSe/MSe naming convention to identification/quantitation [2012-06-06 Wed] - second round of naming changes (utils) [2012-06-07 Thu] - Description of package and methodology updated and references [2012-06-07 Thu] ## Changes in version 0.8.14 - Updated package title [2012-06-05 Tue] - removed PLGS vignette [2012-06-06 Wed] ## Changes in version 0.8.13 - more vignette work [2012-06-01 Fri] - added pgfSweave and xtable to Suggests and loaded in vignette [2012-06-01 Fri] ## Changes in version 0.8.12 - updated show MasterPeptides to reflect number of files effectively used [2012-05-28 Mon] - moved MasterFdrResults to S4 framework [2012-05-30 Wed] - MSnbase is now a dependency [2012-05-30 Wed] - vignette updates [2012-05-30 Wed] - synergise now calls filterUniqueDbPeptides even if master, as opposed to filterUniqueMSeDbPeptides [2012-05-30 Wed] - fixes as(, "MSnSet") - peptides sequences are now properly made unique [2012-05-30 Wed] ## Changes in version 0.8.11 - Automatic handling of Masterpeptides objects [2012-05-23 Wed] - Various man updated to describe the above [2012-05-23 Wed] - Now adding vignettes to windows vignette menu [2012-05-23 Wed] - fixed/improved writeMasterPeptides and fixed [tk_]choose.dir in synergise [2012-05-23 Wed] - MasterPeptides must be save as 'rds' with saveRDS to be reusable in synergise/Synapter [2012-05-23 Wed] ## Changes in version 0.8.10 - updated master-related function names by removing explicit reference to HDMSe [2012-05-16 Wed] - new AllGenerics.R and AllClasses.R files [2012-05-16 Wed] - removed selection param to makeMaster [2012-05-16 Wed] - new makeMaster returns an instance of class 'MasterPeptides' [2012-05-16 Wed] ## Changes in version 0.8.9 - new synergise verbose parameter [2012-05-11 Fri] - filterUnique[HDMSe|MSe]DbPeptides new verbose param [2012-05-11 Fri] - started method documentation in Synapter.Rd [2012-05-11 Fri] - import Vennerable::Venn [2012-05-15 Tue] - updated makeMasterHDMSe file - now has a 'selection' parameter, fixes issue [#27](https://github.com/lgatto/synapter/issues/27). [2012-05-15 Tue] ## Changes in version 0.8.8 - man/vignette updates [2012-05-02 Wed] - added PLGS data input to vignette, contributed by Pavel [2012-05-02 Wed] - added Pavel's PLGS_Data_Processing.pdf slides as vignette [2012-05-03 Thu] - added Biobase import to benefit of addVigs2WinMenu [2012-05-03 Thu] - new plgsGuide() function to access the PLGS_Data_Processing vignette [2012-05-03 Thu] - fixed gui ppm.by label (issue [#25](https://github.com/lgatto/synapter/issues/25)) [2012-05-03 Thu] - License is GPL-2 [2012-05-03 Thu] - vignette improvements [2012-05-03 Thu] ## Changes in version 0.8.7 - added Nick's email to vignette [2012-04-30 Mon] - worked on gui - tree widget now expands when resizing window [2012-04-30 Mon] - added makeMasterHDMSe and estimateMasterFdr cross references [2012-05-01 Tue] - continued vignette [2012-05-01 Tue] - added synapterTiny test data [2012-05-01 Tue] - synapterTinyData to load and initialise the test data [2012-05-01 Tue] - synapterGuide sortcut to open vignette [2012-05-01 Tue] - synergise example (notrun, though) [2012-05-01 Tue] ## Changes in version 0.8.6 - Testing if model exists before findEMRTs/searchGrid [2012-04-27 Fri] - added fdr method choice in synergise [2012-04-27 Fri] - synergise code updates and documentation [2012-04-27 Fri] - work on vignette and new bib file [2012-04-27 Fri] - added package documentation and updated start-up message [2012-04-27 Fri] - added utils in imports [2012-04-27 Fri] ## Changes in version 0.8.5 - 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] - TODO - maybe add fdr method choice in synergise - DONE v 0.8.6 ## Changes in version 0.8.4 - new inspectPeptideScores function [2012-04-26 Thu] - finished gui code - synapterGUI exported [2012-04-27 Fri] - tested synapterGUI until report generation [2012-04-27 Fri] - TODO - avoid loading fasta db twice in filterUniqueDbPeptides ## Changes in version 0.8.3 - fixes getIdStats - now stops if any NA are found [2012-04-25 Wed] ## Changes in version 0.8.2 - fixed typo in data.frame column name [2012-04-25 Wed] ## Changes in version 0.8.1 - new masterFdr function that computes merged FDR - still under construction [2012-04-06 Fri] - updated Synapter.Rd [2012-04-23 Mon] - 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] - estimateMasterFdr (was masterFdr) is functional [2012-04-24 Tue] - estimateMasterFdr output stored in MasterFdrRes S3 class [2012-04-24 Tue] - TODO Investigate NA p-values - DONE - bug fixed in v 0.8.3 ## Changes in version 0.8.0 - added separate add[HD]MSeIdStats method [2012-04-06 Fri] - added separate filterUnique[HD]MSeDbPeptides method [2012-04-06 Fri] - added separate filterUnique[HD]MSeSeq method [2012-04-06 Fri] - new makeMasterHDMSe function [2012-04-06 Fri] - new Master field in .Synapter class [2012-04-06 Fri] - new loadMasterData function [2012-04-06 Fri] - modifed plotFdr and plotPepScores if master [2012-04-06 Fri] - updated Synapter constructor for master [2012-04-06 Fri] - new setMaster method [2012-04-06 Fri] - renames filterUniqueDBpeptides to filterUniqueDbPeptides and added filterUnique[HD]MSeDbPeptides methods in interface [2012-04-06 Fri] - fixes getPepNumbers for master HDMSe [2012-04-06 Fri] ## Changes in version 0.7.8 - renamed plotQvalues to plotFdr [2012-04-05 Thu] - new getFdrStats method [2012-04-05 Thu] ## Changes in version 0.7.7 - non-unique matched features now get NAs except for the first column (Function) [2012-04-04 Wed] - changed FDR adjustment; it is now possible to choose between 'BH' (default), 'Bonferroni' and 'qval' - see issue [#22](https://github.com/lgatto/synapter/issues/22) [2012-04-04 Wed] - updated plotQvalues accordingly [2012-04-04 Wed] - 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 - default span set to 0.05 [2012-03-26 Mon] - fix in setBestGridParams [2012-03-27 Tue] ## Changes in version 0.7.5 - fixed bug in getBestGridParams when what != "auto" and mutliple solutions [2012-03-26 Mon] - type in Synapter.Rd [2012-03-26 Mon] - changed ppm and nsd defaults in searchGrid to reflect defaults in synergise and gui [2012-03-26 Mon] - new 'object' parameter in synergise [2012-03-26 Mon] - updated inputFiles accessor (names and order) [2012-03-26 Mon] - fixed bug in searchGrid when using 'n' [2012-03-26 Mon] ## Changes in version 0.7.4 - using "model" as default parameter selection method [2012-03-23 Fri] - new "auto" parameter selection model - uses "model" and if multiple pairs, uses best "details" if any of ppm/nsd match [2012-03-23 Fri] - remove parameter selection method in gui - using auto [2012-03-24 Sat] - update html report - provide ppm and nsd values selected from grid search and auto method [2012-03-24 Sat] - updates to Synapter.Rd [2012-03-25 Sun] ## Changes in version 0.7.3 - dropped synergize spelling; too annoying when autocompleting [2012-03-22 Thu] - when computing grid details, checking if x["1"] or x["-1"] are NA and replacing by 0 [2012-03-22 Thu] - fixed bug in detail grid [2012-03-22 Thu] - now setting best params in synergize [2012-03-23 Fri] ## Changes in version 0.7.2 - synergi[s/z]e continued [2012-03-21 Wed] - also create a grid based on grid details. This actually fixes a bug in getBestGridParams 'details' search [2012-03-21 Wed] - Removed filterUniquePeptides from loadData, forgot to do that in version 0.7.1 [2012-03-21 Wed] - finished synergi[s|z]e [2012-03-22 Thu] Changes IN VERSION 0.7.1 - synergi[s/z]e definition [2012-03-08 Thu] - GUI implementation [2012-03-10 Sat] - cleaned performance method [2012-03-20 Tue] - 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 - using filtered HDMSePeptideData (was mfHDMSePeptideData) to do the matching; mf[HD]MSePeptideData have been dropped for Synapter class [2012-03-07 Wed] - new dims method [2012-03-07 Wed] - best grid parameter selection based on +1/(+1 + -1) proportion -f correct unique identifications (issue [#18](https://github.com/lgatto/synapter/issues/18)) [2012-03-07 Wed] ## Changes in version 0.6.0 - fixed bug when providing filenames to Synapter [2012-03-06 Tue] - added 'n' parameter to searchGrid to specify a number of features to be used for the grid search [2012-03-06 Tue] - Test if n ] nrow(HDMSe peptides), warn and use all HDMSe peptides [2012-03-06 Tue] - moved some parameter initialisation from searchGrid method to searchGrid interface [2012-03-06 Tue] - new filterUniqueDbPeptides method; this is NOT done anymore when the data is loaded [2012-03-06 Tue] ## Changes in version 0.5.3 - new write[HD]MSePeptides methods [2012-02-17 Fri] ## Changes in version 0.5.2 - added require(MSnbase) in setAs [2012-02-14 Tue] - removed pre/post-fix peptides - is not an issue [2012-02-14 Tue] ## Changes in version 0.5.1 - new setAs method to coerce a Synapter instance into an MSnSet object [2012-02-14 Tue] - added MSe prot FPR filter when calculating performance [2012-02-14 Tue] ## Changes in version 0.5.0 - filtering HDMSe unique peptides [2012-02-12 Sun] - added explicit values to be set for setPpmError and setRtNsd in Synapter man example [2012-02-13 Mon] - filtering pep score (q-val) AND prot FPR (NEW) before matching EMRTs and calculating performance [2012-02-13 Mon] - filtering HDMSe unique peptides [2012-02-13 Mon] - fasta file is also asked for when creating instance [2012-02-13 Mon] - Filtering unique (i.e. non duplicated peptide sequences) is now done when data is loaded, after db unique peptide filtering, to get rid -f pre/post-fix cases (like ABCD and ABCDXXXX) that are not removed by filterUniqueDbPeptides/dbUniquePeptideSet. [2012-02-13 Mon] - keeping common HDMSe/MSe peptides filter is not included in merge Peptides (filterPepSeq removed) [2012-02-13 Mon] - removed (private) filter and idStats parameters [2012-02-13 Mon] - updated documentation [2012-02-13 Mon] - updated performace; removed duplicates count as there are no duplicated sequences/precursor.leIDs anymore [2012-02-13 Mon] - removing duplicated assigned EMRTs; these rows in the matched results dataframes are identified with a -1 [2012-02-13 Mon] - new getLog method [2012-02-14 Tue] - updaed show method [2012-02-14 Tue] Changes IN VERSION 0.4.7 - fixed 'performance' typo in Synapter man [2012-02-09 Thu] - fixed bug in performance/getBestGridValue (issues [#5](https://github.com/lgatto/synapter/issues/5) and [#6](https://github.com/lgatto/synapter/issues/6)) [2012-02-10 Fri] - Updated performance method [2012-02-10 Fri] - Added p/q-values to 'light' merged output [2012-02-10 Fri] ## Changes in version 0.4.6 - HDMSePeptideData is updated (predictRt and sdRt columns) when rt is modelled. [2012-02-09 Thu] - 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] - doHDMSePredictions now returns a list. [2012-02-09 Thu] - added a subet parameter to searchGrid [2012-02-09 Thu] - added a performace method (see issue [#1](https://github.com/lgatto/synapter/issues/1)) [2012-02-09 Thu] ## Changes in version 0.4.5 - removed extra plotRtDiff un Synapter example [2012-02-07 Tue] - 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] - added writeMergedPeptides/writeMatchedEMRTs file argument examples. [2012-02-07 Tue] - PpmError and RtNsd checked/set only for plotFeatures(, what = "some") and not what = "all" anymore. [2012-02-07 Tue] - 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] - grd2 is now computed using new MatchedEMRTs columns [2012-02-07 Tue] - function to get assignment details [2012-02-08 Wed] - 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] - code clean-up: remove old gridSearch call and definition [2012-02-09 Thu] ## Changes in version 0.4.4 - fixed writeMatchedEMRTs/writeMergedPeptides(..., what = "full") [2012-02-07 Tue] - Synapter constructor has filenames argument [2012-02-07 Tue] ## Changes in version 0.4.3 - continued documentation [2012-01-31 Tue] [2012-02-01 Wed] - added plotRtDiffs in example [2012-02-01 Wed] - added warning and nsd[1:3] selection in plotRt model [2012-02-01 Wed] - fixed bug in filterPepSeq; wring MSe dimensions where writton to log [2012-02-03 Fri] - new getEMRTtable method [2012-02-03 Fri] - added ... to plotRtDiffs to be passed to hist [2012-02-03 Fri] ## Changes in version 0.4.2 - Matched EMRTs dataframe cols class is set explicitly based -n HDMSePeptideData and MSePep3DData cols classes [2012-01-30 Mon] - Grid search on percentage of correct assignments [2012-01-30 Mon] - updated grid getters/setters accordingly [2012-01-31 Tue] ## Changes in version 0.4.1 - added legend to plotFeature(..., what="some") [2012-01-27 Fri] - added protein false positive rate functionality [2012-01-27 Fri] ## Changes in version 0.4.0 - introducing ReferenceClasses implementation [2012-01-13 Fri] - filterPepScore takes medianRndScore and stdRndScore as separate parametres instead as a list (params) [2012-01-14 Sat] - fixed a typo in makeSynapterReport [2012-01-16 Mon] - changed several function parameters from input$... into ... [2012-01-17 Tue] - further changes to gridSearch, doHDMSePredictions and findMSeEMRTs to integrate with ref classes implementation [2012-01-17 Tue] - rationalised findMSeEMRTs and gridSearch 'sapply' loops [2012-01-17 Tue] - new keepUniqueSpectrumIds function, now called explicitely before gridSearch and findMSeEMRTs [2012-01-18 Wed] - Testing that changes produce same makeSynapterReport results than version 0.3.2 [2012-01-17 Tue] - added identification p/q-values calculation and qvalue and multtest in imports [2012-01-23 Mon] - global filtering is now done when data is loaded; can also be done manually [2012-01-23 Mon] - removing PLGS pepscore filtering and HDMSe log input [2012-01-24 Tue] - added qvalue and peptide score plots [2012-01-24 Tue] - Synapter ref class interface using S4 methods [2012-01-25 Wed] - Doing mass error filtering on the individual peptide files instead of merged data. [2012-01-26 Thu] - mf[HD]MSePeptideData is not initialised when files are loaded [2012-01-26 Thu] - Documentating new interface [2012-01-26 Thu] - added getRtQs and plotRtDiffs [2012-01-27 Fri] ## Changes in version 0.3.2 - save intermediate filtering tables [2011-12-23 Fri] - added ... to plotLowess2 [2012-01-09 Mon] ## Changes in version 0.3.1 - changed figures url to relative [2011-12-22 Thu] - added synapter version and date to report output [2011-12-22 Thu] - updated filter.error.ppm to specify column name to use as filter [2011-12-22 Thu] - new mass error plot [2011-12-22 Thu] - added orignal nrows in filtering summary table [2011-12-22 Thu] - when provided, htmldir is now created automatically [2011-12-22 Thu] ## Changes in version 0.3.0 - modified rt range calculation [2011-12-20 Tue] - modified feature plot to incorporate rt and mass ranges [2011-12-20 Tue] - adjusted lowess plots ylims to rt modelling range [2011-12-20 Tue] - saving light result tables [2011-12-21 Wed] - added option to perform grid search over ppm and nsd to maximise the number of unique matches [2011-12-21 Wed] - added full range feature plots [2011-12-21 Wed] ## Changes in version 0.2.0 - fixed bug when input was not called 'input' [2011-12-16 Fri] - can now set output directory in makeSynapterReport [2011-12-16 Fri] - using CairoSVG [2011-12-16 Fri] ## Changes in version 0.1.0 - initial release [2011-12-15 Thu]