NEWS.md
In lgatto/synapter: Label-free data analysis pipeline for optimal identification and quantitation

Synapter 2.21

Render fragmentmatching.Rmd with rmarkdown::html_document() (see #139)

Synapter 2.17

put commented code chunk back in

fix error in vignette

Update Laurent's email address

Synapter 2.5

Use BiocManager::install [2018-07-16].

New version for Bioconductor devel

Synapter 2.4

New version for Bioconductor release

Synapter 2.3

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

Partly revert 95f4094 because MSnbase:::utils.applyColumnwiseByGroup is gone.

Synapter 2.0

Version bump for Bioc release version 3.5.

Synapter 1.99

update show,MasterPeptides to check of there's a fragmentlibrary slot before trying to access it <2017-04-19 Wed>

update NEWS file <2017-04-11 Tue>

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.
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 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 and #74.

Misc

Allow to use an RDS instead of a fasta file as 'Unique Peptides Database', adds createUniquePeptideDbRds; closes #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 [2014-04-30 Wed].
Add rescueEMRTs functions; replaces the argument mergedEMRTs in findEMRTs; closes #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 [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 [2015-03-29 Sun].
Add synapterPlgsAgreement to find agreement between synapter and PLGS; closes #73.
Introduce modelIntensity to correct systematic intensity shifts (similar to modelRt); closes #116.

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 [2015-07-26 Sun].
Use just unique peptides in master creation (see #107) [2016-01-23 Sat].
New rmarkdown based reports for synergise1 (synonym to synergise) and synergise2.

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 for details) [2016-01-23 Sat]
Fix retention time model calculation in plotFeatures(..., what="some") [2014-04-28 Mon].

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) [2016-10-16 So].
Replace hwriter by rmarkdown report in synergise; closes #120. [2016-10-17 Mon]

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 [2015-07-26 Sun]
Remove "light" version of writeMergedPeptides and writeMachtedPeptides (now always the full data.frame is saved; see #95) [2016-10-16 Sun]
Update synapterTiny and synapterTinyData [2016-10-16 So]

Synapter 1.13

Update call to nQuants to accomodate changes in MSnbase (see commit #ce637b87e491a2f4c9f93490b2f4c7027cbfce16) <2016-02-29 Mon>
Defunct synapterGUI <2016-02-29 Mon>

Bioc devel 3.2

Synapter 1.12

Bioc release 3.1

Synapter 1.11

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>

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

update cross reference to qvalue::plot.qvalue in Synapter man page; closes #86 [2015-03-31 Tue]

use biocstyle [2015-01-23 Fri]
use requireNamespace [2015-01-23 Fri]

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]

Only suggesting tcltk and tcltk2, as gui is now deprecated [2014-11-21 Fri]

Deprecating synatperGUI [2014-11-10 Mon]
Directing questions to the Bioc support site [2014-11-10 Mon]

new devel version for Bioc 3.1

Synapter 1.7

Deprecating synatperGUI [2014-11-10 Mon]
Directing questions to the Bioc support site [2014-11-10 Mon]

Synapter 1.5

Enable setting number of missed cleavages (closes #53) [2014-03-24 Mon]

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) [2014-03-19 Wed]

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]

biocViews update

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]

typo in vignette [2014-02-18 Tue]

new devel version for Bioc 2.14

Synapter 1.3

estimateMasterFdr now support list of vector as pepfiles [2013-09-27 Fri]
import(MSnbase) [2013-09-27 Fri]

Updated references. [2013-07-05 Fri]

fixed bug when using findEMRTs = "copy" [2013-05-30 Thu]

Reporting total number of peptides in dbUniquePeptideSet. Fixes issue #41. [2013-05-13 Mon]
New mergedEMRTs arg in findEMRTs. Closes issue #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]

Bioc 2.13 devel version bump

Synapter 1.2

Bioc 2.12 stable version bump

Synapter 1.1

updated references [2013-03-22 Fri]

added citation [2013-03-21 Thu]
vignette uses knitr engine and scrartcl class [2013-03-21 Thu]

knitr 1.0 compatibility, based on Dan's updates [2013-01-15 Tue]

added note about tcl BWidget package in synapterGUI man [2012-10-04 Thu]

fixing vignette [2012-10-02 Tue]

new devel version bump [2012-10-01 Mon]

Synapter 0.99

updated ref in package man (2) [2012-09-14 Fri]
updated Synapter show method to display short log [2012-09-14 Fri]

updated ref in package man [2012-09-11 Tue]

bumping version number to take all previous changes into account [2012-08-29 Wed]

fixed build problem on windows [2012-08-27 Mon]
updated refs in vignette [2012-08-28 Tue]

using dev='pdf' in vignette and removing tikzDevice (not on CRAN anymore) from Suggests[2012-08-16 Thu]

added tikzDevice suggestion for vignette [2012-08-15 Wed]

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]

vignette update with summary table [2012-07-17 Tue]
vignette update with additional PLGS slides [2012-07-17 Tue]

updated vignette [2012-07-12 Thu]
removed README.org file [2012-07-12 Thu]
added github page in DESCRIPTION [2012-07-12 Thu]

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]

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]

use log2 for t.test [2012-07-05 Thu]
updates to vignette [2012-07-06 Fri]

git/svn integration messing up and testing [2012-07-03 Tue]
late night testing [2012-07-03 Tue]

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]

Latex typo in vignette [2012-06-11 Mon]
Dan's suggestions for [2012-06-13 Wed]

bump version for Bioconductor submission [2012-06-08 Fri]

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]

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]

Updated package title [2012-06-05 Tue]
removed PLGS vignette [2012-06-06 Wed]

more vignette work [2012-06-01 Fri]
added pgfSweave and xtable to Suggests and loaded in vignette [2012-06-01 Fri]

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]

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]

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]

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. [2012-05-15 Tue]

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) [2012-05-03 Thu]
License is GPL-2 [2012-05-03 Thu]
vignette improvements [2012-05-03 Thu]

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]

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]

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

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

fixes getIdStats - now stops if any NA are found [2012-04-25 Wed]

fixed typo in data.frame column name [2012-04-25 Wed]

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

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]

renamed plotQvalues to plotFdr [2012-04-05 Thu]
new getFdrStats method [2012-04-05 Thu]

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 [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]

default span set to 0.05 [2012-03-26 Mon]
fix in setBestGridParams [2012-03-27 Tue]

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]

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]

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]

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]

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) [2012-03-07 Wed]

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]

new write[HD]MSePeptides methods [2012-02-17 Fri]

added require(MSnbase) in setAs [2012-02-14 Tue]
removed pre/post-fix peptides - is not an issue [2012-02-14 Tue]

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]

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 and #6) [2012-02-10 Fri]
Updated performance method [2012-02-10 Fri]
Added p/q-values to 'light' merged output [2012-02-10 Fri]

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) [2012-02-09 Thu]

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]

fixed writeMatchedEMRTs/writeMergedPeptides(..., what = "full") [2012-02-07 Tue]
Synapter constructor has filenames argument [2012-02-07 Tue]

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]

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]

added legend to plotFeature(..., what="some") [2012-01-27 Fri]
added protein false positive rate functionality [2012-01-27 Fri]

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]

save intermediate filtering tables [2011-12-23 Fri]
added ... to plotLowess2 [2012-01-09 Mon]

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]

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]

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]

initial release [2011-12-15 Thu]

lgatto/synapter documentation built on Sept. 28, 2022, 6:53 a.m.

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lgatto/synapter Label-free data analysis pipeline for optimal identification and quantitation

NEWS.md In lgatto/synapter: Label-free data analysis pipeline for optimal identification and quantitation

Synapter 2.21

Changes in version 2.21.1

Synapter 2.17

Changes in version 2.17.3

Changes in version 2.17.2

Changes in version 2.17.1

Synapter 2.5

Changes in version 2.5.2

Changes in version 2.5.0

Synapter 2.4

Changes in version 2.4.0

Synapter 2.3

Changes in version 2.3.1

Synapter 2.1

Changes in version 2.1.1

Synapter 2.0

Synapter 1.99

Changes in version 1.99.2

Changes in version 1.99.1

Changes in version 1.99.0

New features

Ion mobility/Grid search.

Fragment matching

Misc

Improvements

Bugfixes

Internal changes

Removed functions/arguments

Synapter 1.13

Changes in version 1.13.1

Changes in version 1.13.0

Synapter 1.12

Changes in version 1.12.0

Synapter 1.11

Changes in version 1.11.2

Changes in version 1.11.1

Synapter 1.9

Changes in version 1.9.5

Changes in version 1.9.4

Changes in version 1.9.3

Changes in version 1.9.2

Changes in version 1.9.1

Changes in version 1.9.0

Synapter 1.7

Changes in version 1.7.0

Synapter 1.5

Changes in version 1.5.7

Changes in version 1.5.6

Changes in version 1.5.5

Changes in version 1.5.4

Changes in version 1.5.3

Changes in version 1.5.1

Changes in version 1.5.0

Synapter 1.3

Changes in version 1.3.4

Changes in version 1.3.3

Changes in version 1.3.2

Changes in version 1.3.1

Changes in version 1.3.0

Synapter 1.2

Changes in version 1.2.0

Synapter 1.1

Changes in version 1.1.5

Changes in version 1.1.4

Changes in version 1.1.3

Changes in version 1.1.2

Changes in version 1.1.1

Changes in version 1.1.0

Synapter 0.99

Changes in version 0.99.15

Changes in version 0.99.14

Changes in version 0.99.13

Changes in version 0.99.12

Changes in version 0.99.11

Changes in version 0.99.10

Changes in version 0.99.9

Changes in version 0.99.8

Changes in version 0.99.7

lgatto/synapter
Label-free data analysis pipeline for optimal identification and quantitation

NEWS.md
In lgatto/synapter: Label-free data analysis pipeline for optimal identification and quantitation