Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

This is a list of recent commits to git.bioconductor.org, the master(development) branch of the Bioconductor GIT repository.

This list is also available as an RSS feed (master branch), and RSS feed (release branch)

Package: Biostrings
Commit: 1eca6e2c4c3405cdcb6ba3fd8a83a04a9706596d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-19 05:13:39
Commit message:

 minor tweak to "show" method for PairwiseAlignments objects
 
Package: cytofkit
Commit: 2a9fac33d2d9140fd68629063f281c3bab3d8be3
Author: MattMyint <matthewmyint1993@gmail.com>
Date: 2018-01-12 09:34:50
Commit message:

 global scaling fixes
 
Package: PureCN
Commit: f95e754ce43912f93bc8ecbea67b78a9c954d38a
Author: lima1 <mriester@gmx.de>
Date: 2018-01-19 01:42:42
Commit message:

 Throw exception when normalDB is outdated.
 
Package: PureCN
Commit: ec6f11d9108b33e000a1229b8160ed60189eaaf0
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-18 18:28:37
Commit message:

 Replaced voom normalization with GATK4's tangent normalization (https://github.com/lima1/PureCN/issues/18)
 
Package: PureCN
Commit: 36ccafcffe32d7890e7afaf8be927652918c4cfb
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-16 04:56:56
Commit message:

 Added support for GATK4 CollectFragmentCounts in readCoverageFile.
 
Package: Biostrings
Commit: 750f92a0fcaef5fa998876db628ac3ca091806d9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-19 00:19:08
Commit message:

 Add the alignedPattern() and alignedSubject() getters for extracting
the aligned patterns and subjects from a PairwiseAlignments object.

Unlike aligned(pattern()) and aligned(subject()), alignedPattern()
and alignedSubject() do NOT trim globally aligned sequences. The
fact that aligned(pattern()) and aligned(subject()) trim the deleted
extremities of globally aligned sequences as been a nuisance and a
source of complain for many years. The addition of alignedPattern()
and alignedSubject() is a response to this.

The "show" method for PairwiseAlignments objects now uses
alignedPattern() and alignedSubject() internally to display the
untrimmed globally aligned pattern and subject.

The "as.character" method for PairwiseAlignmentsSingleSubject objects
was modified to do as.character(alignedPattern(x)) so does not trim
globally aligned patterns anymore.
 
Package: GENESIS
Commit: e9f54c813269922bb6e6a75c549c8f0ca4e8f64d
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 21:19:58
Commit message:

 version bump
 
Package: GENESIS
Commit: fdd56eb39b340a337f9a48eb365e96a0e1754ebd
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 21:17:16
Commit message:

 fix missing file links in man pages
 
Package: S4Vectors
Commit: 60e9d32bda4617ad9362dc81fb4b1fce6eae2db2
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-01-18 21:16:39
Commit message:

 prepare_objects_to_concatenate() in .concatenate_vectors()
 
Package: BiocCheck
Commit: cdfffcd49b8e2abf0f7c758c98b6a5a4743fcc62
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-18 20:39:39
Commit message:

 version bump & contributor
 
Package: BiocCheck
Commit: 1c8cdf3d4bdd152fe558cee4b8883aa37d026ea6
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-18 20:39:24
Commit message:

 remove unused code
 
Package: BiocCheck
Commit: 65bd6bffba5b7c32d118e4a977919d4a9db186ac
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-18 20:38:52
Commit message:

 parse only .R files for library(), sapply(), etc.
 
Package: CrispRVariants
Commit: b9b733e5fc94392f71bf659545ca94750d23dc8d
Author: Helen Lindsay <helen.lindsay@uzh.ch>
Date: 2018-01-18 20:28:19
Commit message:

 Easier specification of plotting order
 
Package: chimeraviz
Commit: c924e0d3f3e484cc854b4b92b9deb8ba05a525e2
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-01-18 20:02:09
Commit message:

 Bump version to trigger build
 
Package: chimeraviz
Commit: 276e38cfc319c6adae0d5979ddd8e8ca6c54d9a1
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2018-01-13 17:26:29
Commit message:

 Support the latest output version from STAR-Fusion
 
Package: BiocFileCache
Commit: ca1a4824d895a345a5fceaec93a53687d37313dd
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 19:39:58
Commit message:

 Fix a test

   - access time changed because of access, compare all values but this
 
Package: GWASTools
Commit: e57a2df7f571fe3518020deb73c883c108920031
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 19:25:03
Commit message:

 version bump
 
Package: GWASTools
Commit: 343ea244ce303a7eed906b0c39403ad78da3499e
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-01-18 19:20:30
Commit message:

 fix links to other packages in man pages
 
Package: XVector
Commit: 31f780777e421d223eca259641098f228818219d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-18 17:37:28
Commit message:

 The "concatenateObjects" method for XVector objects must set the 'offset'
slot of the returned object to 0L.
 
Package: BPRMeth
Commit: bf3691bf16d9bee349159a77c5e62ee3540d9f4f
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-18 17:25:07
Commit message:

 Bump version
 
Package: BPRMeth
Commit: c221ae878a16678f7d77820e4d481aa13ac710f3
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-18 17:24:36
Commit message:

 Fix VB implementation numerical issue with Gamma priors
 
Package: BPRMeth
Commit: cdc84c0040a245df3193b84bebdefa19a3c0c615
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-18 14:34:51
Commit message:

 Minor changes in VB implementation
 
Package: annotatr
Commit: c4b4858ef649a5a9ac447d3171f5b33b01d7599d
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-18 16:34:12
Commit message:

 Suggest TxDb and OrgDb packages

* This saves users some space with package installations.
* The requireNamespace() approach is taken with an error indicating which package needs to be installed. 
Package: annotatr
Commit: fbae1e0b3940fd496b84e1fc23b3be6a0176a13e
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2018-01-18 16:06:57
Commit message:

 Bugfix: For builtin_ functions, need to use annotatr::

* This solves a problem I didn't originally understand that was posed in the Bioc support forums. 
Package: ndexr
Commit: cde4facdd0f254bfe338f8dd111e5f3d2450d703
Author: Florian J. Auer <florian.auer@med.uni-goettingen.de>
Date: 2018-01-18 15:48:39
Commit message:

 fixed build error caused by 'metadata:properties' now being optional
 
Package: qpgraph
Commit: 791f057d9cc4815fda0d5c36189fbf9d559ae2f2
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-01-18 15:41:45
Commit message:

 Added a qpPathWeight-dspMatrix method.
 
Package: rhdf5
Commit: 762af749e83d5a1c9fb14b0cfa828f82429b4621
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-18 15:30:24
Commit message:

 Adding platform specific print statments for 64bit ints.
 
Package: rhdf5
Commit: 8530a8fa40125d48875f01c6721d3dee79a1dcef
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-18 13:30:16
Commit message:

 Experiment with windows specific print statements
 
Package: rhdf5
Commit: 5cef56e10152469253a692a4f1b8ed4ad3222f2a
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-12 16:33:35
Commit message:

 Added tests for h5closeAll()
 
Package: ndexr
Commit: 2d8a91afcb1ec26fa15efae4ce2fa161113b6a14
Author: Florian J. Auer <florian.auer@med.uni-goettingen.de>
Date: 2018-01-18 15:16:45
Commit message:

 fixed build error caused by 'metadata:properties' now being optional
 
Package: omicsPrint
Commit: dba2cdcbfcb98a152e8947486aa360d403db6d52
Author: DavyCats <davycats.dc@gmail.com>
Date: 2018-01-18 09:10:16
Commit message:

 handle NA in phasing
 
Package: BiocFileCache
Commit: 51c044801d26f8bbca54df97fac9cb16c72dfc28
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 14:01:33
Commit message:

 Fix .httr_get_cache_info

  - updating to return etag and last_modified time, need to update error patch to have same structure
 
Package: BiocFileCache
Commit: e58d870545543c5e7dcd59f320a353aa95ecd423
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 13:10:48
Commit message:

 bfcinfo and bfcquery display full rpath

   - rpath will still be stored as relative but display fully
 
Package: BiocFileCache
Commit: 53fd3d69e33397c825e824a88ac4c034a7a4356a
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 12:14:54
Commit message:

 Add section in vignette

   - for best practice when using within a package
 
Package: BiocFileCache
Commit: bfda0df8a7eb0244f3e2cd431afcf8ef1d2b71cf
Author: lshep <shepherl@gmail.com>
Date: 2018-01-18 11:55:42
Commit message:

 Merge branch 'convertFromDF'
 
Package: BiocFileCache
Commit: 0b722783985635b1ade39c0903df366500a530ba
Author: lshep <shepherl@gmail.com>
Date: 2018-01-16 19:59:32
Commit message:

 Add function makeBFCfromDF

  - converts a data.frame to a BiocFileCache object
 
Package: BiocStyle
Commit: c070ef71d4a46b96892cec6f16ff4fc1cb593dfa
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-18 12:01:59
Commit message:

 version 2.7.6
- switch documentation to roxygen2
 
Package: oposSOM
Commit: dd2904e6a5472d358fd89c25021d148ed06c63cb
Author: hloefflerwirth <wirth@izbi.uni-leipzig.de>
Date: 2018-01-18 10:15:53
Commit message:

 oposSOM 1.17.1: Crucial fix for unstable ensembl database availability.
oposSOM 1.17.0: Bumped version number by Bioconductor + few minor changes.
oposSOM 1.15.3: Bugfixes for Chromosome Expression Plots and PCM.
oposSOM 1.15.2: Bugfixes for Chromosome Expression Plots and ICA.
 
Package: synapter
Commit: bd1c294deaac81d2daab37f5c8986b9777cb15e1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-17 20:43:30
Commit message:

 Fix charges argument in .requantifyTheoreticalDistribution
 
Package: synapter
Commit: a18bcd4af745c0e4cb3e986d81b307ee99b457dd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-17 20:31:25
Commit message:

 Use  instead of
 
Package: synapter
Commit: e57f0aa8af33f6b0b006c7143deb0fb24722ab62
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-17 20:24:02
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: synapter
Commit: 68c480d1ceeea8ff71c99e68f45b8b96c49e0a2b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-05-29 19:03:15
Commit message:

 bump version and update NEWS.md
 
Package: synapter
Commit: b41a33d114d761b1833ee2644840cf86487f38da
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-05-29 18:55:48
Commit message:

 partly revert 95f4094, because MSnbase:::utils.applyColumnwiseByGroup is gone
 
Package: synapter
Commit: 331e3ee74844330b1c16e4d030efdfc5797ac397
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-19 11:08:12
Commit message:

 remove travis badge for 2.0 branch [ci skip]
 
Package: synapter
Commit: 6613b5bc6032f7b02df0536bce5bf410ea5b0cf5
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-19 09:17:34
Commit message:

 update show,MasterPeptides to check of there's a fragmentlibrary slot before trying to access it
 
Package: synapter
Commit: 8a5c39544564924eb84885039beb17a9b0ba33e3
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 16:04:58
Commit message:

 add news back
 
Package: synapter
Commit: 9dc214408847f7a388af0b72f16030024f369113
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 15:08:16
Commit message:

 fix news version
 
Package: synapter
Commit: d8e263bd833c0ede484d623b29b770c9f770e867
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 15:06:55
Commit message:

 only news md
 
Package: synapter
Commit: a402debc5b3e5e306764df58ed9920a96113842e
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-11 15:05:46
Commit message:

 update news
 
Package: synapter
Commit: 5bc07eaf28125f615227751bdbf0787ea4e1256e
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-07 07:02:27
Commit message:

 add files to inst/doc to fix vignette build
 
Package: synapter
Commit: 9444fa764f09ae35faaf71f46fd38f27a4ece37b
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-06 15:52:39
Commit message:

 add/update links to github page
 
Package: synapter
Commit: 9cf05d77c49ed3f120a0fbf1aea81a270365a262
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 11:10:23
Commit message:

 add unit test for .cumsumIntensities
 
Package: synapter
Commit: 4bca1ebe8c653249ab3163d72f7de81dadedf1e9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 11:03:56
Commit message:

 add unit test for filterEmptyFragments
 
Package: synapter
Commit: 177ae8be4d084a5aa08a232253e57876319f4020
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 10:52:34
Commit message:

 add unit tests for .getSpectrum and .sumAllPeakCounts
 
Package: synapter
Commit: 5812a7877ffa43f99e745e914b865fe1e6e13bbc
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 10:07:58
Commit message:

 add @noRd to avoid warning about invalid documentation path
 
Package: synapter
Commit: b08e483b5325cc705d82cab0a089ed59c4eae366
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 10:03:32
Commit message:

 add docs/ directory; closes #132
 
Package: synapter
Commit: 95451aa350a9cd799dee544732540a812726f5aa
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 09:49:32
Commit message:

 add branch-specific gitignores as described at https://lgatto.github.io/branch-specific-gitignore/
 
Package: synapter
Commit: 9eb9d03510b5d3c28ddfe3f4a018f25cb02281a7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 09:13:55
Commit message:

 remove biocView GUI
 
Package: synapter
Commit: eca574414cf639219552a1cf6b95a9e3fb41acf0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-05 08:57:01
Commit message:

 avoid NOTE: \examples lines wider than 100 characters
 
Package: synapter
Commit: 608ba0e0fcd3e42cdd781c607e5ead61330dd013
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-04 10:36:35
Commit message:

 remove results="asis"
 
Package: synapter
Commit: 6a960aa1f571e107af672a9999bd636d8b36c59c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-04 09:36:44
Commit message:

 use synobj2RData() to access synobj2
 
Package: synapter
Commit: 05bd448142c1f7d854a67509bb3b2f1b0b26802f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-04 09:32:19
Commit message:

 Revert "replace synobj2 by synobj3"

This reverts commit 91f6a71e741ef08ebfaa3cb0859b7525fedab3f2.
 
Package: synapter
Commit: f73e92a2107723025f35ee47f2b290544b179f62
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-04 08:34:00
Commit message:

 Merge branch '2.0' of github.com:lgatto/synapter into 2.0
 
Package: synapter
Commit: 8c33fe29d8f509e4a47ff8c9979fe229a62def81
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-04 08:32:12
Commit message:

 suggest synapterdata 1.13.2
 
Package: synapter
Commit: aa512d0381755c57c2a71cdf4a439db25bb32a7c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:54:45
Commit message:

 Merge branch '2.0' of github.com:lgatto/synapter into 2.0
 
Package: synapter
Commit: b6bd69c3fede570e6f5d3259aa701a4cf7eddd5e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:54:37
Commit message:

 limit output to the first 13 lines
 
Package: synapter
Commit: 7771324d6deea55669d14d4deb6a63cfd2bdc11b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:13:01
Commit message:

 adapt mergeMaster unit test to new span.rt/span.int arguments
 
Package: synapter
Commit: 7e7d81e266d38da1cd05d05019eb19d3e1fa6cab
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 22:03:09
Commit message:

 fix class version assignment
 
Package: synapter
Commit: 91f6a71e741ef08ebfaa3cb0859b7525fedab3f2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-04-03 21:58:31
Commit message:

 replace synobj2 by synobj3
 
Package: synapter
Commit: da20825e06521aebba88753b55b9c02dc16df541
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-03 14:05:30
Commit message:

 depend on synapterdata 1.13.1 for synobj3
 
Package: synapter
Commit: ccbd8414fcf674e9992d0e2afb6a519f1c209160
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-24 13:00:51
Commit message:

 replace (m)apply by for loops
 
Package: synapter
Commit: 5cf9a32b717eab176d04d0886b1ba307c914f086
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-24 12:27:27
Commit message:

 fix calculateGridPerformance for categories with 0 occurence; fix #134
 
Package: synapter
Commit: b6088c5dd543ee64a142a632f856b34501ba73a0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-12 16:51:57
Commit message:

 set missedCleavages=2 as default for synergise2
 
Package: synapter
Commit: 42a08518d52cdbd81440ce2694e5316a01b29b77
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-04 21:40:18
Commit message:

 rerun roxygen
 
Package: synapter
Commit: b51c9a32bd62a7fe3ed7a96620dc22b90e66aa2a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-03-04 21:40:04
Commit message:

 add span.rt and span.int to makeMaster
 
Package: synapter
Commit: f9154667a0c6b333bfc7e07162e880a7a183a7d6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-02-08 01:16:39
Commit message:

 define constant for classVersion to avoid regression in .isCurrent
 
Package: synapter
Commit: e0cbdf7906e60dcf2602ae7730c04303d430607b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-25 13:05:50
Commit message:

 extend performance report [ci skip]
 
Package: synapter
Commit: bf56392fd92ed573b44fbc515ed65ddb0a03d52a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-25 13:05:28
Commit message:

 just print performance2 if verbose=TRUE; [ci skip]
 
Package: synapter
Commit: d5ddba1fcd4b479eea36e81617559d39c638cfd5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-22 17:10:40
Commit message:

 set IisL=FALSE; closes #133
 
Package: synapter
Commit: a0f5a3d65d2b48743fd060be25f7586fd3dcedb2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-18 23:16:44
Commit message:

 fix header level [ci skip]
 
Package: synapter
Commit: b4a0bf2edd1d74f8a90baa2fc2d6da99c7cf2627
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-18 15:22:05
Commit message:

 don't validate MSnExp in .spectrumXml2spectra; see also lgatto/MSnbase#183
 
Package: synapter
Commit: 43f256fc43201c863ad20862a7b61761f4bcafe9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 22:41:19
Commit message:

 add Authors@R [ci skip]
 
Package: synapter
Commit: ef25be92cb1b582f86f202b1a6142d31d31c6266
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 22:17:59
Commit message:

 first synapter2 vignette draft; see #124
 
Package: synapter
Commit: c8d9122e5174b6d2860e76c56708eddba5561ff0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 21:48:14
Commit message:

 plotIntensity instead of plotRt
 
Package: synapter
Commit: 68327e31770011a93ab1c4e16f4e7146170a5b3a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 19:46:26
Commit message:

 fix correctIntensity call in requantify
 
Package: synapter
Commit: 5b909548032af90094bd4d4067bc900ece5e42f0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 19:36:05
Commit message:

 allow synapterPlgsAgreement for MSnSets with just 1 sample
 
Package: synapter
Commit: a9983a09172033e13088b41c0a0ec3c56d4b9280
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 18:43:14
Commit message:

 fix unit tests for verbose=TRUE
 
Package: synapter
Commit: fa57c514b60420c6588148420e4c021e0449b4a9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 17:06:36
Commit message:

 replace verbose=TRUE by verbose=interactive()
 
Package: synapter
Commit: 726b5f86d18aa1fe4c0ccfd2d8bb74921c6f5a00
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 17:04:19
Commit message:

 fix object name
 
Package: synapter
Commit: 5a31811f16643ba3ee3ef5b203254441cb460c43
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 13:58:28
Commit message:

 pass grid.imdiffs.* arguments to .synergise
 
Package: synapter
Commit: e52a3f0c06b3531ed8ed42800a86bcbc4b66d81f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 13:02:18
Commit message:

 add first stub synapter2 vignette [ci skip]
 
Package: synapter
Commit: 3117da1f091c6b4ba5392c4f0be15a938a971778
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 12:54:24
Commit message:

 append newline
 
Package: synapter
Commit: 9d8e07fc31011239bd1a079ccac563505ddaafe7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 12:03:24
Commit message:

 correct file path for create_synobj2.R
 
Package: synapter
Commit: 43c2173c7e1b2e5994716e82bcd0ec486ed768df
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 12:03:04
Commit message:

 don't use svg to save space
 
Package: synapter
Commit: c9f5978f22cc4b7b6b6a7974954d3722b3b45a1b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 11:59:35
Commit message:

 modelIntensity just works after findEMRTs
 
Package: synapter
Commit: f05fd59cec1a05678c9eae66a15c8a9db87ef5b7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 11:45:36
Commit message:

 add synapter2workflow flowchart; closes #130
 
Package: synapter
Commit: d1ef702d0e30cd121c17602496253f8c875addfe
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 09:10:09
Commit message:

 add fragment library hint to NEWS.md [ci skip]
 
Package: synapter
Commit: c381ee6fbcd369e4e2159a73c12b73b9eec097a3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:55:38
Commit message:

 replace NEWS by NEWS.md [ci skip]; closes #79
 
Package: synapter
Commit: a91a214c5982bf197fd5dc5af554c066ccdbc94d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:54:31
Commit message:

 add NEWS.md and docs to .Rbuildignore [ci skip]
 
Package: synapter
Commit: cfd766e3f4fd59c84c69398ceac05c1369b3ed71
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:06:20
Commit message:

 coding style [ci skip]
 
Package: synapter
Commit: 512fa2415a952abf29613a03219863a9c5991f83
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-17 08:05:30
Commit message:

 Revert "remove useless comparison"

This reverts commit 415b5997f9a0cc6f07a5ab3c5004d525970b06ec.
 
Package: synapter
Commit: 893f68742146c84a44422033a1e44503696ea39b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-16 20:44:47
Commit message:

 remove wrong eval=FALSE
 
Package: synapter
Commit: 415b5997f9a0cc6f07a5ab3c5004d525970b06ec
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-16 19:02:11
Commit message:

 remove useless comparison
 
Package: synapter
Commit: 7564bd7bd166b1610caf92a36b75240abff5c566
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-16 13:57:08
Commit message:

 convert synapter vignette to markdown
 
Package: synapter
Commit: 2bb31fb19f45faf76eebd149b36190ed3157e1f6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-01-14 17:01:21
Commit message:

 convert fragmentmatching vignette to markdown
 
Package: synapter
Commit: 43edaf8d6958049bbd74149c622cb4ff4840ff63
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-23 13:41:52
Commit message:

 avoid unnecessary copy in calculateGridPerformance [ci skip]
 
Package: synapter
Commit: 517237ea364783cbb5563886564e881f05692100
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 21:21:05
Commit message:

 Merge branch 'master' into 2.0 [ci skip]
 
Package: synapter
Commit: 0028c401a44cc43accdd741385239d3eb722b91f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 21:02:50
Commit message:

 add identfragments/quantspectra to synergise2 documentation
 
Package: synapter
Commit: 89bd40990dcec338063deefc91207ea3667ad7f7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 20:45:21
Commit message:

 include sessionInfo in reports
 
Package: synapter
Commit: 6d7910b846224a9aed74a459bd873bfa3dab84a3
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-12-22 11:01:14
Commit message:

 update readme
 
Package: synapter
Commit: bbbfc1934e22f8c285645abbeb129100c8127aa0
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-12-22 10:24:08
Commit message:

 ignore travis config when building pkg
 
Package: synapter
Commit: 704c22ab2abb8afc90b251d8957b97749288c013
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-12-22 10:23:29
Commit message:

 add travis config file
 
Package: synapter
Commit: 60fe95fe6343172cf5f7b92023f89b72518c4366
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2016-12-22 10:20:48
Commit message:

 Merge pull request #131 from lgatto/travis

add .travis.yml 
Package: synapter
Commit: 1bdef7dc504ca5b0d34b36ac33c219d54fc81b61
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-22 09:39:42
Commit message:

 add .travis.yml
 
Package: synapter
Commit: 267986e43a39bd71f574bcb566e3454d7ce9f249
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-08 21:07:57
Commit message:

 remove duplicated rescueEMRTs call
 
Package: synapter
Commit: 151cdcb5e81cdf6b1326ba28cda092356dba583e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-08 15:19:58
Commit message:

 fix brackets
 
Package: synapter
Commit: 1deacfe3b5f76953986d5b5f02e4f91e6f2332e0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-02 20:13:02
Commit message:

 don't write useless rownames to csv
 
Package: synapter
Commit: b7b03df0640985c3c7de3f501e44c0f68cbe9543
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-02 20:10:12
Commit message:

 reset defaults for fm.min{Common,Delta} and fix calculation of their threshold selection; fixes #128
 
Package: synapter
Commit: 496c9ffbabfea2421d711d848a3572d75e59ec85
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-12-02 19:46:21
Commit message:

 set IisL=TRUE as default in synergise2
 
Package: synapter
Commit: 5056230acbc2f01d02d1efd7695cfda859d61950
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-11-18 11:27:57
Commit message:

 replace default Spectrum2 ctor by C level replacement; see lgatto/MSnbase#171
 
Package: synapter
Commit: b6972770ef860d94c41bc8a9430982fd97525cf5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 17:59:06
Commit message:

 export synergise2
 
Package: synapter
Commit: bafb30d1a4b5ef1dd83945733ba8e564a8c648ff
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:55:37
Commit message:

 remove Makefile for vignettes
 
Package: synapter
Commit: 78eefd164f506924e818a54c8e02f37fbd533c3a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:55:17
Commit message:

 add missing space
 
Package: synapter
Commit: e31f8ecdad47b80dee673b13475d304ad4386819
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:53:37
Commit message:

 fix fragment filtering log message
 
Package: synapter
Commit: b906a278a36f3298f793a62dfa3b2ed1487a54b2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 16:12:02
Commit message:

 filter fragments by intensity in synergise2
 
Package: synapter
Commit: 0ff943f7864c42a033e0bda028cd7e60bab3d982
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:53:30
Commit message:

 fix tempdir call
 
Package: synapter
Commit: 0de2a243658073e56f3372e85c41c952c44a7942
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:19:34
Commit message:

 remove GUI from vignette
 
Package: synapter
Commit: 80a21877042f21d7ddafa381a3b2eae60d10a90e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:14:13
Commit message:

 remove useless NEWS entries
 
Package: synapter
Commit: 03cfac28be40ed56827a1bc5808f4ef8b06666e9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:04:34
Commit message:

 remove GUI hint
 
Package: synapter
Commit: 188b0dd8dbd5502b3857c60e9b0812f2995f0cc0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 15:03:29
Commit message:

 use ion mobility in plotFeatures
 
Package: synapter
Commit: a64ad310b2d60f30bba9ce83ba5a64bf101d8e01
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-28 14:31:15
Commit message:

 remove sentence about GUI; closes #121
 
Package: synapter
Commit: c8be9c6abb0db4d56a3e0c3e6cbffca550de8594
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-26 18:01:28
Commit message:

 call .correctIntensity automatically and hide the it from the user; closes #126
 
Package: synapter
Commit: a203a192c026a897e1c4af0e6006fba16f1b0332
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-26 01:41:06
Commit message:

 add IdentFragmentFile and QuantSpectrumFile to show output; closes #125
 
Package: synapter
Commit: 154b472bd33f8fdb320b63fefeac0b2dec75b9e6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-25 16:35:35
Commit message:

 add missing synergise2 report file; #119
 
Package: synapter
Commit: 175b2aec7936bd03da102ff2c73196d5dbdad3f1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-25 16:32:44
Commit message:

 add synergise2 man page; #119
 
Package: synapter
Commit: ccf6c363ca55f18e798238b33787544101a6d1dd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-25 16:32:02
Commit message:

 disable 3D gridsearch for synergise1
 
Package: synapter
Commit: e69ada857e3bcf8607daac6f2ab1338b3cc160cd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-25 16:26:15
Commit message:

 add synergise2; closes #119
 
Package: synapter
Commit: c73fe37c1ae4fcaada5cf34c398281aa9e3f62d2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-25 15:45:21
Commit message:

 add synergise1 to fragmentmatching vignette
 
Package: synapter
Commit: fbb66dd65458e0750d6d780a1b3745245efee71a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-21 11:21:41
Commit message:

 extract common synergise code from synergise1.Rmd
 
Package: synapter
Commit: a51dedfb273a0cf10c4edcd3e813d813c218508f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-20 11:16:40
Commit message:

 add fragmentMatchingPerformance
 
Package: synapter
Commit: 3b504bc01a39cc0fc7b67c8d7bdec963b0f7f34f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-19 11:46:19
Commit message:

 update fragmentmatching vignette; closes #83
 
Package: synapter
Commit: 307053351873b9eda3e4fde259346c1e242284ae
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-19 09:43:24
Commit message:

 call normalizePath to ensure rmarkdown finds the files after changing the working directory
 
Package: synapter
Commit: a50d6cda03c2c5e5503f8f2da1db90ed30758287
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-17 17:44:41
Commit message:

 fix no visible binding for global variable/no visible global function
 
Package: synapter
Commit: ec816a56e0936f4f44f0bda48e540aab4ad01966
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-17 17:39:57
Commit message:

 set df=NULL for fragmentlibrary creation
 
Package: synapter
Commit: 4c13a29a2c7005e65c2207d52450d2fa94036273
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-17 17:27:39
Commit message:

 add correctIntensity documentation
 
Package: synapter
Commit: 35b39129f14d7a471c9e26d352de22aaaace5988
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-17 17:26:54
Commit message:

 add rescaleForTop3 documentation
 
Package: synapter
Commit: 910c2c9176ca2b256455f65626ad80e6a68a3f39
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-17 16:12:02
Commit message:

 import from graphics and stats to avoid WARNING in R CMD check
 
Package: synapter
Commit: d24cdd08e15cbaec4a0ce09ffdcb224fbbc3c50f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-17 15:31:14
Commit message:

 replace hwriter by rmarkdown report; closes #120
 
Package: synapter
Commit: 4e3ca5e32c9275fe9f29313a2cf73f1cdc6be359
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-16 15:45:47
Commit message:

 fix Makefile targets
 
Package: synapter
Commit: d004917a67765a9edf2befa249beaeb70ae2a1f8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-16 15:26:58
Commit message:

 update synapterTiny and synapterTinyData
 
Package: synapter
Commit: 25cfd47e6952dbd6733d7dfbdb4ddd7b705fcf7e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-16 14:45:16
Commit message:

 adapt synergize to new grid search; closes #81
 
Package: synapter
Commit: a77ce51af4c8244006ed074b11dcb9c8141c5f7b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-10-16 14:12:23
Commit message:

 remove light version of write{Merged,Matched}Peptides; closes #95
 
Package: synapter
Commit: 56b53e43162362ece0cb3eaa77f7aad9fe0deaad
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-09-06 18:38:57
Commit message:

 add ylim to plotLowess{Data,Model}
 
Package: synapter
Commit: 6e128f1b381361f89bf0eb5daf5c30bd6e46cb1f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-09-05 17:08:11
Commit message:

 use intenRatio
 
Package: synapter
Commit: e387252b15f63de581a3ad63a616756f2e332b9b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-09-05 10:05:08
Commit message:

 add plotIntensity; see #116
 
Package: synapter
Commit: 38362d12dc7f7cfb589b729f697dee50108f0fc1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-11 16:22:21
Commit message:

 add intensity correction; see issue #116
 
Package: synapter
Commit: 6eb682094f30ec0cc404c8af7915e58cd2c3abd6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-08 14:22:01
Commit message:

 fix ms2 line range; bug introduced in c271bbee6a78ba15a7ff13ecbbd7fd462d7b4935
 
Package: synapter
Commit: 87c4643ebd3abb78db00d505140d61ce40ec5e3b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-08 11:09:58
Commit message:

 fix variable names in loess predict
 
Package: synapter
Commit: c271bbee6a78ba15a7ff13ecbbd7fd462d7b4935
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-07 15:47:34
Commit message:

 some code reformating in .readSynapterSpectrumXml
 
Package: synapter
Commit: 92dcf3cacb999f9dadc55177bc2e34b74353e4db
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-07 15:46:33
Commit message:

 fix NAMESPACE
 
Package: synapter
Commit: 6bcdca3fde82ff6ca79ca5f5c4aec2161aba0004
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-04 10:39:24
Commit message:

 fix unit tests
 
Package: synapter
Commit: 71c4faeba9bed07a87c81f0a3a88aa3b227401d6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-04 09:42:18
Commit message:

 apply intensity correction during master creation; see #116
 
Package: synapter
Commit: f8d701a4a2d53ed152cde219e79ab34b855c4474
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-04 09:40:30
Commit message:

 rename rawRetTimeModel in loessModel
 
Package: synapter
Commit: 8965f150f6d11dd11de85fd7281332203276f154
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-08-03 11:54:36
Commit message:

 fix roxygen comment
 
Package: synapter
Commit: 473c0c6381e6413059749aff3bd08055b3bb9513
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-07-13 10:00:59
Commit message:

 remove tcltk dep
 
Package: synapter
Commit: 9c6ff6d22656b965e59bf63b8163bbd7a919cc86
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-06-29 19:54:17
Commit message:

 add showAllPeptides to plotFragmentMatchingPerformance; closes #115
 
Package: synapter
Commit: 85a78521d7b6df09b2dc1057ddc30db736168852
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-06-13 19:39:35
Commit message:

 fix .isotopicDistr2matrix for all NA
 
Package: synapter
Commit: 52ada6906468611e7d875b5a12276b61cbb90bb0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-05-25 19:28:53
Commit message:

 ignore missing runs for requantification
 
Package: synapter
Commit: 5d89912d30675438b25016ded1082409e3efdaf5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-05-22 17:15:58
Commit message:

 fix onlyForSaturatedRuns in rescaleForTop3
 
Package: synapter
Commit: 6edfecd5f9387633758cbe91d7a85b55c70682cf
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-17 20:13:31
Commit message:

 calculate FragmentMatchingDiff for all non-unique matches; closes #114
 
Package: synapter
Commit: 8d4c87bd5f1adce4e42c8d6bc308968ad42fa8ad
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-11 20:45:52
Commit message:

 add missing dot; fixes #113
 
Package: synapter
Commit: a0c0e3e9a46b71eb1126c3402e83d6dacd9bf44e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-10 16:02:30
Commit message:

 add rescaleForTop3; see #39
 
Package: synapter
Commit: 9fba7b5e87ab96fd2a2205aadeede5aac8a87c72
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-10 14:39:46
Commit message:

 update documentation
 
Package: synapter
Commit: 25135f65f6131101e34d65e814d07e3126dacbdd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-09 20:12:42
Commit message:

 return NA for requantified sum == 0; see #39
 
Package: synapter
Commit: 045752e8b927d9ba5d5940accbe8c168850c47e7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-09 20:11:48
Commit message:

 use run with most common ions and highest counts as reference; see #39
 
Package: synapter
Commit: 3b79c05e6dc3424ed2bfb898217d53bb09b2513b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-04 18:10:28
Commit message:

 introduce .names2chargesIsotopes
 
Package: synapter
Commit: 272343587ff0fb9fa3491997eb6d9a7f4568bd36
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-04-04 17:48:06
Commit message:

 sort columns of isotopic patterns by charge state
 
Package: synapter
Commit: 921e37271512b6145e0ca394441f7fc20bff1dd3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-29 19:13:29
Commit message:

 don't introduce new values for missing entries; a second time; see #39
 
Package: synapter
Commit: 73120bdc880fddeeb3028a5ed398b21b1d5e3aed
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-25 18:09:13
Commit message:

 remove useless function .sumIsotopes
 
Package: synapter
Commit: 95f409461249294699d4135567eb15d5cd201e1b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-25 17:39:59
Commit message:

 use MSnbase:::utils.applyColumnwiseByGroup
 
Package: synapter
Commit: 252a8dc0602a62b3fdcebdef76ed2371a1f21bac
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-25 17:14:57
Commit message:

 remove useless returns
 
Package: synapter
Commit: 17c2564a345e56131397b756e90fbbe07ea9e823
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-25 17:12:43
Commit message:

 don't sum isotopes across charge states before calculated theoretical distribution; see #39
 
Package: synapter
Commit: fc51081078b378430dcc216a7bd8ca0e3c892685
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-23 17:55:03
Commit message:

 don't introduce new counts for missing values; see #39
 
Package: synapter
Commit: 52979a3b39d90905f89354b367dead1451ab5f25
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 23:07:20
Commit message:

 add requantifyAll argument for th.* methods
 
Package: synapter
Commit: 3aa115983a2080a552264033f286d3064e074a4e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 22:15:39
Commit message:

 update manual page
 
Package: synapter
Commit: 7529501ffa39a728f3f731a461a9b86908d60e15
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 22:15:26
Commit message:

 fix syntax error
 
Package: synapter
Commit: 87435d7a3cda533e5fdb0e94af17d48daf0011ba
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 22:10:51
Commit message:

 fix arguments
 
Package: synapter
Commit: ca8bd7d49b781c1ce7d6341792ce64d7d39c2674
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 22:02:09
Commit message:

 export requantify and synapterPlgsAgreement methods
 
Package: synapter
Commit: c5006b919dea43a4d8890db9536c6eb5f4633804
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 21:48:21
Commit message:

 turn requantify into a method and add documentation
 
Package: synapter
Commit: fee51ce2a9fa594da8af284db7a79e147d209c5c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 20:45:03
Commit message:

 correctly handle NA values in all th methods
 
Package: synapter
Commit: e41ea9b6b00afabf1952cc087339eee7c8f6d066
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-21 20:44:13
Commit message:

 pass ... arguments to .requantifySum
 
Package: synapter
Commit: ef32e1313d3ace8a89ed707271864a4c6f6c63fd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-20 15:26:21
Commit message:

 finally reintroduce #99; closes #106
 
Package: synapter
Commit: cd5bbf7385bd6dda195ff260f1c590d905ba77a4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-20 11:17:58
Commit message:

 rerun roxygen
 
Package: synapter
Commit: 0b46e9a50819ed544c16081a8b29043b8e581804
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-20 11:17:35
Commit message:

 add synapterPlgsAgreement documentation
 
Package: synapter
Commit: b96861931afea9524c231ca57bc1845925262b25
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-20 10:35:51
Commit message:

 add missing synapterPlgsAgreement unit test
 
Package: synapter
Commit: dfd846402f5f901dd3f249d73680cd316c97e5c4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-20 10:33:38
Commit message:

 turn synapterPlgsAgreement into a method and add unit test
 
Package: synapter
Commit: b3e5893958f6821d5dfb2eb45c890e73a909ff02
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-01 16:59:31
Commit message:

 fix merge
 
Package: synapter
Commit: 943e1fdea994ac2389f6982c47f269cdf62acd6a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-03-01 16:57:06
Commit message:

 Merge branch 'master' into 2.0

Conflicts:
	DESCRIPTION
	NEWS
	R/gui.R
	R/synapter-interface.R
	man/synapterGUI.Rd
 
Package: synapter
Commit: f2c86adcefb4650ce2f8435ca7fa5e6a6631ff81
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-02-29 23:17:49
Commit message:

 Update nQuant and remove synapterGUI

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>
 
Package: synapter
Commit: 4d0e74b54566abfbd99d50141b3456b82d596d6c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-24 19:49:10
Commit message:

 remove useless line
 
Package: synapter
Commit: 874797256762ffa95c16c4e69cab83fd107630d1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-24 19:14:10
Commit message:

 add unit test for flatMatchedEMRTs' na.rm argument
 
Package: synapter
Commit: 994171c83a49e6f4e7cfebc35b8d9c01487d648b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-22 20:29:12
Commit message:

 add filterNonUniqueIdentMatches to NAMESPACE
 
Package: synapter
Commit: 79a1a4bc155c6bbad99020d7d0a4a78f0c2f5a6f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-22 20:00:32
Commit message:

 add filterNonUniqueIdentMatches; closes #111
 
Package: synapter
Commit: 59e1b414ccaf36a7af8a043c68eb869486c3b160
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-22 19:52:54
Commit message:

 fix typo
 
Package: synapter
Commit: c6d3750ae216fe016a827cc21b05924e6f5d5227
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-22 18:23:33
Commit message:

 add .duplicated2
 
Package: synapter
Commit: 88ab27824f04c4218a353907b003ec222d3acde4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-02-08 20:31:51
Commit message:

 remove plotFragmentMatchingDiff from man page; close #109
 
Package: synapter
Commit: 8821226a258ed6708d7465d6643ee04cd06eb2a8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-31 19:59:14
Commit message:

 rescue non-matched EMRTs data from Pep3D data; fix #108
 
Package: synapter
Commit: 9dbe5c2e80b3f3b114c73365b27047dc546f8ab5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-31 19:58:03
Commit message:

 fix typo
 
Package: synapter
Commit: 27edf562dd687aaf04bf764d85122576f6d225ec
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-25 19:53:00
Commit message:

 add missing fData to requantify unit tests
 
Package: synapter
Commit: 00a3f194f34e02b60930f8a19368c86f3936c805
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-24 11:05:52
Commit message:

 add NEWS entries for #107
 
Package: synapter
Commit: 3100e465ecfb78bd58b533351c1e75157baa13c8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 14:09:08
Commit message:

 handle verbose argument correctly in loadIdentOnly
 
Package: synapter
Commit: 2cb729e40dea05b3ff57034add16c57bc81d46f6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 13:59:28
Commit message:

 rewrite estimateMasterFdr
 
Package: synapter
Commit: 6dfc072deabe24d2fb68d963ad9c60036b776653
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 13:58:40
Commit message:

 add .masterFdrSummary
 
Package: synapter
Commit: ab4708014e93e973ae7756fd67f0ebcbe87579b2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 13:16:41
Commit message:

 introduce .peptideMatrix
 
Package: synapter
Commit: ef06556ca0704efdeeedea34b6921c22ad4f6990
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 12:41:31
Commit message:

 introduce .calculatePeptideFileCombinations
 
Package: synapter
Commit: 027c131ade07d2271c055ecc720442a4b15bcaad
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 12:40:57
Commit message:

 fix typo
 
Package: synapter
Commit: c88d12e236c629ff8ad0b53943558e216d33e072
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 12:04:11
Commit message:

 add missing span argument
 
Package: synapter
Commit: 1ce0248e078e00e246624ede17fe1e3a82b91828
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 11:56:27
Commit message:

 add comment
 
Package: synapter
Commit: 5bf716833596cda0c4b4ccab24deef1dffd247d1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-23 10:47:23
Commit message:

 Revert "change sign for prediction"

This reverts commit c56ea82f961c437f6bd5a1df76be38e3e625995b.
 
Package: synapter
Commit: efac3a4f97a403638a624e89914acb475a1a94de
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-21 19:40:11
Commit message:

 add .filterDuplicatedPeptideSequences
 
Package: synapter
Commit: c56ea82f961c437f6bd5a1df76be38e3e625995b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-20 18:01:18
Commit message:

 change sign for prediction
 
Package: synapter
Commit: 8456e6af2401959c952545a2eda8f21ffc0f1b9a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-19 10:17:09
Commit message:

 add internal rawRetTimeModel
 
Package: synapter
Commit: ec081fd09e33c83cfa774a131354533cae76d112
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-18 20:39:53
Commit message:

 reintroduce orders object
 
Package: synapter
Commit: 4c568542ac7247317cace635f96c66380509d1d7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-18 17:53:58
Commit message:

 fix regeneratePrecursorLeId call
 
Package: synapter
Commit: 44d91b142cf96fcddb67c7b74a5623ff26a60c32
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 21:26:55
Commit message:

 replace modelRetTime by direct loess call to avoid integer overflow by predict(..., se=TRUE)
 
Package: synapter
Commit: 7cde00fd4f11ea936c435b06fc1f5fe35c29c32e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 11:06:57
Commit message:

 adapt makeMaster to new helper functions
 
Package: synapter
Commit: 6083738321680c072c83894f9bc44cc2fa831770
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 11:02:48
Commit message:

 add .regeneratePrecursorLeId
 
Package: synapter
Commit: 3b9b94631a9f043916ac4a45b031fd46f6305d4a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 10:50:20
Commit message:

 add .mergeMaster
 
Package: synapter
Commit: 4b8cb42208da6bf01bb8478b9e90ea30c8c9652c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 10:13:20
Commit message:

 create .mergePeptideData
 
Package: synapter
Commit: af483f15387c6235bbd36f0ed86a03886d76ae25
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 09:28:17
Commit message:

 remove useless return statement
 
Package: synapter
Commit: ed92a8b3e6c605a3044f4b788b1c7137575c9c44
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 09:27:51
Commit message:

 create orderForMasterModels function
 
Package: synapter
Commit: cc0a20f6abd67bc56fd4ed58b113c2912be0c69a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 09:09:43
Commit message:

 add unit test for modelRetTime
 
Package: synapter
Commit: 5ced9549ced38f60bb17c264ee1c702af0d3fa42
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 08:44:47
Commit message:

 adapt arguments of modelRetTime
 
Package: synapter
Commit: 32bfee45d7f2d7d1fce799ee418a5fc3e4b4f34a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2016-01-17 08:23:12
Commit message:

 remove useless return statements
 
Package: synapter
Commit: 9eb76573c98977dd8115fcffc17c33434243aea8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-12-12 13:26:39
Commit message:

 don't update fvarLabels automatically
 
Package: synapter
Commit: c04dd665d5f97b2b41dc7a8391c7b11287f2d387
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-12-04 19:55:43
Commit message:

 rewrite requantify
 
Package: synapter
Commit: bf98f7c0ea6006395d06557855d47405eff04491
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-12-02 21:27:55
Commit message:

 first new implemenation of .requantifySum and .requantifyReferenceRun
 
Package: synapter
Commit: 4105c68bc4e6f7b2d3107834d717ab56d97bd0ee
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-12-02 20:01:49
Commit message:

 replace .splitIsotopicDistr by .isotopicDistr2matrix
 
Package: synapter
Commit: cd01eaa9654fb80dfacf99bd0dbe2c29db3f6349
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-11-29 19:45:11
Commit message:

 this time write a few test first
 
Package: synapter
Commit: efa7799f49d0197b664f85e28fcfb2637ebba53e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-11-29 17:58:39
Commit message:

 remove isotopes that are not in the reference run
 
Package: synapter
Commit: 877b7c15283951a722bfbbe29a618d58adebd642
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-11-29 00:09:25
Commit message:

 use readr::cols_only instead of self-written header handler
 
Package: synapter
Commit: f59e7189b070226823d7ea64e6c356ab83c28ac5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-27 16:51:38
Commit message:

 Merge branch 'master' into 2.0

Conflicts:
	DESCRIPTION
	NEWS
 
Package: synapter
Commit: 21a2bece6cb4baac435dc4f996c762f3abab2e7c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-27 16:43:22
Commit message:

 fix check for available columns (bug introduced in 1.11.1)
 
Package: synapter
Commit: 5c6aa6c056b40f2be504e57d1556da73faf4c56d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-15 10:40:07
Commit message:

 add unit test for .recalculateFragmentIntensities
 
Package: synapter
Commit: 50be61f95aec3cb0f98be4f471604eabdeb3d193
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-15 10:39:30
Commit message:

 remove useless (wrong) rownames
 
Package: synapter
Commit: ca53ff8aef946dff413dc47e7817f21039099502
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-15 10:39:17
Commit message:

 fix order of removing duplicates
 
Package: synapter
Commit: 6af3e9329aee20a3a26fe638276a7337242d5b53
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-15 09:53:46
Commit message:

 fix merged syntax error
 
Package: synapter
Commit: e1c4470b164261ce537471fbba1f5c1110eefddb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-11 07:20:49
Commit message:

 Merge branch 'master' into 2.0

Conflicts:
	DESCRIPTION
	NEWS
	R/synapter-interface.R
 
Package: synapter
Commit: 35c485a57188d45897c2e0cb1b7158a0d94a25a7
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-09-07 22:44:46
Commit message:

 check and subset cols when coercing synapter to msnset
 
Package: synapter
Commit: 8dc442fed1fb8c8b9938583e6a62e66cbd8abf83
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-02 20:58:25
Commit message:

 correct rounding of intensities; fixes #101
 
Package: synapter
Commit: 704c8396bbf389a006aa2d235f17ab628fffe0de
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-09-02 20:35:59
Commit message:

 add requantification by reference run; see #39
 
Package: synapter
Commit: a2319b9c983027ba76aecd3720ee4ceaf5a1aa7e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-23 10:36:25
Commit message:

 ignore file extenstion of compressed files in 'as'
 
Package: synapter
Commit: e001c274982a4c42cf4a29173845098d8933d203
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-23 09:28:34
Commit message:

 ignore non-existing column names
 
Package: synapter
Commit: e5f029f83771d0ba480b39cbd1641fb6c4253146
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-20 19:07:01
Commit message:

 export requantify; #39
 
Package: synapter
Commit: 815e2be300bcef1265e50eafb1836ff7db6a4209
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-10 18:51:20
Commit message:

 import product.rank column; fixes #100
 
Package: synapter
Commit: 7526f12d2cefed3061c464b1fbeb37da524397c7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-09 15:56:15
Commit message:

 fix NA values in nAgree/nDisagree; #73
 
Package: synapter
Commit: 46de584cf1da82d4d62eb3634c9ba51377877a6f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-05 20:42:35
Commit message:

 use .self as sampleNames for MSnSets; closes #99
 
Package: synapter
Commit: d01b6caee66c1932fabddaed2efcd844987ff59a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-05 20:26:50
Commit message:

 fix calculation of the synapterPlgsAgreementRatio; #73
 
Package: synapter
Commit: 73cb314c3d6e80739742d792f161f531591fbf9b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-08-05 19:42:53
Commit message:

 export synapterPlgsAgreement
 
Package: synapter
Commit: de8846825868bae84a44a33c7a1d475444e3c4e3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-29 20:22:27
Commit message:

 reimport all Pep3D data for non-unique-matches; close #93
 
Package: synapter
Commit: fdfb5ced884f12fe1bd928e2c6b83a0db1ab3a78
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-29 20:07:21
Commit message:

 fix handling of multiple ids in .findSynapterPlgsAgreement
 
Package: synapter
Commit: f572437683fe1a68e12444874fd63abe582e6652
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-28 18:17:38
Commit message:

 add getIdentificationFragments and getQuantitationSpectra; closes #89
 
Package: synapter
Commit: 730b44a9c3d0628bd99827d28eddf8f12bc17bf5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-28 17:44:11
Commit message:

 keep all matched.quant.spectrumIDs; closes #93
 
Package: synapter
Commit: 18b0185867fb896a8042f74de90f1ae863c3a298
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-28 17:40:39
Commit message:

 fix missing Counts for filtering non-unique matches; closes #93
 
Package: synapter
Commit: 8c1cae3c7b3ba1c11049337a2f170eade94c1ded
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-28 14:52:52
Commit message:

 skip unnecessary columns in .readSynapterSpectrumXml
 
Package: synapter
Commit: ce4d107dab00b52113111cb30182d8532b65f2e2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-27 18:12:48
Commit message:

 remove quotes from column headers in csv files; closes #96
 
Package: synapter
Commit: b9685c00983ec8affef3fdaae75b8a4da9a73c3d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-27 18:03:23
Commit message:

 use readr in .readSynapterSpectrumXml as well
 
Package: synapter
Commit: b6cf32842c7a56fa84bf42de48e3484101f33f23
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-26 14:03:32
Commit message:

 add missing product.z column
 
Package: synapter
Commit: 98c3b2f58a400cdd4de0b52bc9ec6b6fa99400c0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-26 13:48:11
Commit message:

 fix some missing functions && rerun roxygen
 
Package: synapter
Commit: 96b66ce18477fbf9100c2b57d87cbae9637dcd89
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-26 13:07:57
Commit message:

 Merge branch 'master' into mergemaster

Conflicts:
	DESCRIPTION
	NAMESPACE
	NEWS
	R/AllGenerics.R
	R/MSnbase-extensions.R
	R/fasta.R
	R/fragmentmatching-functions.R
	R/fragments-functions.R
	R/gui.R
	R/spectrum-functions.R
	R/synapter-class.R
	R/synapter-interface.R
	R/update.R
	R/utils.R
	man/Synapter.Rd
	man/makeMaster.Rd
	man/plotCrossMatching.Rd
	tests/testthat/test_utils.R
	vignettes/Makefile
	vignettes/fragmentmatching.Rnw
 
Package: synapter
Commit: 54b4094f5f9e6e6db115276bece19b7723fa959b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 23:26:10
Commit message:

 Merge branch 'issue67' into 2.0

Conflicts:
	R/utils.R
 
Package: synapter
Commit: 506de168fcaf45e46b28d12f81e18c9627d756bd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 23:17:35
Commit message:

 separate rescueEMRTs in own function; closes #93
 
Package: synapter
Commit: 5296e4057727747d62df351bccfa8e422b524bec
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 22:58:36
Commit message:

 add .rescueEMRTs
 
Package: synapter
Commit: c2695ea8c5e52cbc671426823fdb7f7d3a01a116
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 22:22:14
Commit message:

 Merge branch '2.0' into saturation

Conflicts:
	DESCRIPTION
 
Package: synapter
Commit: f29895aee357be83d7e584b62ce045aa1e747f24
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 22:21:24
Commit message:

 fix verbose output
 
Package: synapter
Commit: d943db7a07c6413b1ecad9d844fa9821c0c21c7c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 22:19:50
Commit message:

 rename Function column into matchedEMRTs; closes #67
 
Package: synapter
Commit: 10df8ade785fad34d835cad70b5b7af3c30aec89
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 21:57:05
Commit message:

 remove ifelse in calculateGridPerformance
 
Package: synapter
Commit: 988298ace90f7b173e5816903c29c19029c635b2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 21:55:57
Commit message:

 use readcsv for final peptide and pep3d; closes #87
 
Package: synapter
Commit: c9bdbf85b7462a70a62c3f2d19f15a76ab2fef40
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 20:52:08
Commit message:

 Merge branch '2.0' into readr
 
Package: synapter
Commit: b0e652a531332654ee89543b88e3e65402bdce92
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 20:49:09
Commit message:

 look up row of [LH]E_ID; fixes #90
 
Package: synapter
Commit: 659c17a7c6e2f759c8c6379c4a55dfdc36e44bd6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-25 11:32:16
Commit message:

 adapt to changed NA behaviour of nchar in Rdevel; fixes #92
 
Package: synapter
Commit: 21916c436944e7c3db3f32c2543e66b591b76dd6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-23 19:41:06
Commit message:

 adapt unit test to change of sep
 
Package: synapter
Commit: 395e6f30f9fd4965d9a3297f73b52492243fa1a9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-23 19:05:01
Commit message:

 Merge branch '2.0' into readr
 
Package: synapter
Commit: 155e8686dc42dfb7946a99c4f23d6cdb99b55a50
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-23 19:04:35
Commit message:

 Merge branch '2.0' into saturation
 
Package: synapter
Commit: 32c245e432c794162c3289114d47c096cc83209a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-23 19:03:40
Commit message:

 remove ionmobility vignette
 
Package: synapter
Commit: 7ef343348ef2dc2eeb42195e5822891e6fc919b1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-20 16:50:29
Commit message:

 readd missing columns
 
Package: synapter
Commit: a2c10a119c25902b0c421dd64aac1fed7df7b9c7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-19 16:30:37
Commit message:

 remove temp file in unit test
 
Package: synapter
Commit: e4cf895b67c7dcfc503e9a2ec54d6bd069f5ef62
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-19 16:29:32
Commit message:

 use readcsv in .readFragments
 
Package: synapter
Commit: 49d3cc7dc648c3ab6982ea4fb98eb60c9a4a76d4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-19 16:17:49
Commit message:

 add readcsv unit tests
 
Package: synapter
Commit: 6d31ca8e89e6fc761a3ef5f9c1618272386c3161
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-07-18 12:24:12
Commit message:

 first attempt to use readr::read_csv instead of base::read.csv
 
Package: synapter
Commit: 27ad79f6777d8423fb34addd877071fb0fccad94
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-04-16 20:02:44
Commit message:

 Bump versions in trunk after creation of 3.1 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@102594 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: a38931d2d9b9637d832f940d284f47277a026ea2
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-04-16 19:42:01
Commit message:

 Bump versions prior to creating 3.1 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@102591 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: 3f79b47a1df1607619b49d991d3444abe8bfb595
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-04 16:50:44
Commit message:

 allow NAs in th.weighted.mean
 
Package: synapter
Commit: 9e25c9f191dbfc2cbd9787dcca1119b9cd040e49
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-04 16:50:30
Commit message:

 rename .requantifyPeptides into .requantifySum
 
Package: synapter
Commit: 1470fbf6561f1be8be32cd622a6163fc67038280
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-04 16:43:53
Commit message:

 add synapterPlgsAgreement; see #73
 
Package: synapter
Commit: e811f8eb4a98d159bd3181f44a827b62efdd13cf
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-04 16:34:12
Commit message:

 add first implementation of requantification; see #39
 
Package: synapter
Commit: 378cee7bc569af890bc92b5ee4bff612116e4e92
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-04 16:29:30
Commit message:

 fix accidentally conversion of Counts from numeric to character in findMSeEMRTs
 
Package: synapter
Commit: f771702f45d1cfecf862cc6bf5dca5dbd7fb4da3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-04 16:27:46
Commit message:

 allow NA values in .splitIsotopicDistr
 
Package: synapter
Commit: 3cb7bd4ce8022e3a40bd413323b02919d86e1d94
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-02 07:46:53
Commit message:

 fix flatMatchedEMRTs test
 
Package: synapter
Commit: 878b93ab969cfd3eae8cb422e034a3fb73efa9a9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-02 07:46:22
Commit message:

 fix matched.quant.spectrumIDs2numeric test
 
Package: synapter
Commit: 0f158fa59f2a62292cfa1c7249eb4667e489435d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-04-02 07:45:54
Commit message:

 add .splitIsotopicDistr
 
Package: synapter
Commit: 67c9d3f62382063b0406adb69f651afd7ea383f5
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-03-31 21:23:06
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@101672 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: 3f5f916d2f27e89aadb5713ee4e72acd5c66d2c4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-03-31 17:59:13
Commit message:

 update link to qvalue::plot.qvalue in man page; closes #86
 
Package: synapter
Commit: 162664ecd5010fe1539860e4bd9147c1094641af
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-03-31 17:46:42
Commit message:

 change order of isotopic distribution reading
 
Package: synapter
Commit: 8be0584aa1d34b4fcdefae733cbfba466210583f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-03-31 17:07:54
Commit message:

 change isotopicDistr format
 
Package: synapter
Commit: 8c94ace1a7702a7e7d87e53384d3ff13ac79fd79
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-03-29 19:59:54
Commit message:

 export isotopic distributions to MSnSet
 
Package: synapter
Commit: b68cdb2e2abff97c35f68c2c78995e3ad8994794
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-03-29 19:38:19
Commit message:

 Merge branch '2.0' into saturation
 
Package: synapter
Commit: 2afa5313581b77e71d034540267dc18991666630
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-03-29 19:11:11
Commit message:

 set Counts of filtered (non-)unique matches to NA; closes #85
 
Package: synapter
Commit: de3f5fa7d34ff8744318bdcd123917db39c8e76a
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-01-23 22:26:54
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@98635 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: 02ae468f92d2d183ec92efd57e0cef05387be622
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-23 22:22:15
Commit message:

 use BiocStyle
 
Package: synapter
Commit: 01b3a64375f5d709f1066492d538ccc2a525081f
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-23 14:30:41
Commit message:

 new dev ver
 
Package: synapter
Commit: cecbc6665e551d2c571ba183e4d1ae3cc7bf6f96
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-01-23 14:29:42
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@98607 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: 4de7403aef3208882f25ae5f25f397ca7da9cb4c
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-23 14:28:34
Commit message:

 fixing warnings
 
Package: synapter
Commit: c33299b0408cfed2290c169bcdff0bd7d3c6abb7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-04 19:29:20
Commit message:

 replace own getExtension by tools::file_ext
 
Package: synapter
Commit: f9c022869421f074865122e03c3aa724f9abd9cd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-04 19:10:21
Commit message:

 import isotopic distribution from Pep3D files
 
Package: synapter
Commit: 14d87a57b354cc0760e2ca1325fbd0ad1f469163
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-04 14:39:06
Commit message:

 remove BiocParallel dependency introduced in 0a17326
 
Package: synapter
Commit: 4a0d52edbe05ce756cdaec58ea9bac79f572b2b3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-03 23:05:31
Commit message:

 add synapterPlgsAgreement column to Synapter and MSnSet object; #73
 
Package: synapter
Commit: 1dec83aa6e01fbf3f9d88e1a876f8c3f77c01182
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-03 22:31:52
Commit message:

 handle multiple matches as 'no_synapter_transfer'; #73
 
Package: synapter
Commit: 91df86fe6a067987a8cf2c823ecedb63cf8b24dc
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-03 16:13:26
Commit message:

 add .findSynapterPlgsAggreement; regarding #73
 
Package: synapter
Commit: 0792f0cf3e813b74898de076c4d9e8a6b891868f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-01-03 12:43:23
Commit message:

 fix Synapter constructor for non-fragment cases

The updated Synapter constructor was not able to create Synapter objects for
runs without fragment and Spectra files.
 
Package: synapter
Commit: e190bfea7c7505895727babddef38d4b3c5d6650
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-12-07 17:29:39
Commit message:

 remove loadIdentificationFragments and loadQuantitationSpectra
 
Package: synapter
Commit: b0b86efc5e8864d3b598925881383d646b00a429
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-12-07 17:24:43
Commit message:

 loading identification fragments and quantitation spectra via Synapter constructor
 
Package: synapter
Commit: d774d963e2d501909de3c27e353b1b9e66c4e8d9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-12-03 18:18:12
Commit message:

 load fragment library from master
 
Package: synapter
Commit: 9fde83a217500c3a5ebde3eb0369b2d396d9f64d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-12-03 18:09:46
Commit message:

 allow master creation without fragment files
 
Package: synapter
Commit: 5a7fc69aa66435d81c2bc7fe03cb0cb377459363
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-27 09:38:27
Commit message:

 remove unused internal functions that filter AA seqs
 
Package: synapter
Commit: efb88f1cc77479516be950d76709b17ed667782d
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-26 23:13:55
Commit message:

 Merge branch '2.0' of github.com:lgatto/synapter into 2.0
 
Package: synapter
Commit: 3b0bbbb4bd6088ac70433f9f641423571f28a179
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-26 23:13:32
Commit message:

 add sgibb as maintainer
 
Package: synapter
Commit: d113e01119a31c148b056611168e00a2921f5f48
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-11-26 23:12:51
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@97169 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: 9c3b3f5e36798c3c99d6b5a3fa0d7e1160d41bce
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-26 23:12:19
Commit message:

 add sgibb as maintainer
 
Package: synapter
Commit: 0fd3c1d8df59d8188c15b8cccfef9271bf07d857
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-11-26 23:10:30
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@97167 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: 897c2e02d39cea454d61c8cec24f5dc091dabb8f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-26 22:54:17
Commit message:

 fix if statement
 
Package: synapter
Commit: 3eb8bb8e0af0d84a279e437bd38a4a32dbd7d420
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-26 22:46:11
Commit message:

 workaround for quant final peptides and pep3 with mismatching intensity values;
affects #42
 
Package: synapter
Commit: 92bde641f39f5d7798b5dd4e4dda05fa71a4ea8f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-24 20:49:54
Commit message:

 remove hidden ion mobility plots
 
Package: synapter
Commit: dc4ab22485f27ca19e4b21bbb2c1dfc435e8a8cd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-24 20:41:38
Commit message:

 Merge branch 'issue72' into 2.0

Conflicts:
	NEWS
 
Package: synapter
Commit: 1f53f7d772978d1a0f0fc5a73b7de2592a57db43
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-24 20:40:57
Commit message:

 rename CrossMatching to FragmentMatching; closes #72
 
Package: synapter
Commit: 7590ab10b64123d730d5f485e652388fcabdafbc
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-23 20:14:09
Commit message:

 adapt vignette to reduced CrossMatching
 
Package: synapter
Commit: a61b89b68e1ed62168795d4c057868a428b5043e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-23 20:13:49
Commit message:

 adapt manual pages to reduced CrossMatching
 
Package: synapter
Commit: 2f3af3ae5d8fbf96f73331fa26544d990a0572a5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-23 20:13:26
Commit message:

 adapt plotCumulativeNumberOfFragments to reduced CrossMatching
 
Package: synapter
Commit: 3962aafaf0924370ec3b93a94fef7882e3c0ffd3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-23 19:52:52
Commit message:

 adapt filter(Non)UniqueMatches to reduced CrossMatching
 
Package: synapter
Commit: 5c1f82b596a41b4c6b1c396c75cf797fa1ef3ee0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-23 19:52:35
Commit message:

 adapt plotCrossMatchingPerformance to reduced CrossMatching
 
Package: synapter
Commit: 6032486ef1a409c94b74b94dfdb8119587c312bd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-22 22:04:39
Commit message:

 adapt plotCrossMatching to reduce CrossMatching
 
Package: synapter
Commit: 310bb3a38e7440aab1a2fb871d2b6c82a3690a50
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-22 20:57:43
Commit message:

 reduce crossMatching to ident fragments vs quant spectra
 
Package: synapter
Commit: 59897aa7bad3a2c635326dd46a3e5822fab5c530
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-22 19:39:39
Commit message:

 replace loadFragmentsCsvFiles/loadSpectrumXmlFiles by loadIdentificationFragments/loadQuantitationSpectra
 
Package: synapter
Commit: c34fe3476ae823e8e7c776e04c0b33084e557342
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-22 19:32:06
Commit message:

 add Versioned as parent class for MasterPeptides and MasterFdrResults
 
Package: synapter
Commit: 371ac8e05edae3dc9a2426088aa03b23b12bebc5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-21 21:03:24
Commit message:

 remove IdentSpectrum* and QuantFragment* fields
 
Package: synapter
Commit: 88f19690dc373bf32aacbd946b8252ad38c6f93c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-21 20:46:29
Commit message:

 Merge branch 'updateSynapterObject' into 2.0

Conflicts:
	NEWS
 
Package: synapter
Commit: de73e66810a372c684036dccbb75c55f759f1b83
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-21 20:37:48
Commit message:

 replace .isSynapterObjectOutOfDate by isCurrent

Use Biobase generic `isCurrent` instead of `.isSynapterObjectOutOfDate` to test
for the correct version. Additionally `isCurrent`/`updateObject` are adapted to
the new `ClassVersion` field.
 
Package: synapter
Commit: e0d5f9c04449fdeeaae5b13f639313ee7e2c7dd3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-21 20:37:39
Commit message:

 add ClassVersion field to Synapter class; closes 78
 
Package: synapter
Commit: f391102c2ec61941e1cf059c7a582177b29e8677
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-21 16:40:49
Commit message:

 new devel version
 
Package: synapter
Commit: e96d7bc42bb61f9b8b860f58e29099f46499b2b8
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-11-21 16:40:17
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@97009 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: d891917b31c3f998f9f04f2c859d5e3589323809
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-21 16:39:09
Commit message:

 bump to version 1.99.0 and only suggest tcltk/tcltk2
 
Package: synapter
Commit: f154d05841e77aef7d69c3b9eb06a6b2fe8dd907
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-21 16:34:19
Commit message:

 Only suggesting tcltk and tcltk2, as gui is now deprecated
 
Package: synapter
Commit: c1cb289a3644258fbce980134d8d874ff61b5cf0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-16 11:57:02
Commit message:

 add NEWS entry
 
Package: synapter
Commit: a7a73002ba03a03221800d454ad225fae864d412
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-16 11:55:44
Commit message:

 Merge branch 'updateSynapterObject' into 2.0
 
Package: synapter
Commit: cca99398de47e001dc068fb91f0404c2777be382
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-16 11:55:03
Commit message:

 replace isSynapterObjectOutOfDate by validObject
 
Package: synapter
Commit: 716dfe9a9178d49cd63d59003909963dbe682fb4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-13 20:27:47
Commit message:

 Merge branch 'fragmentLibrary' into 2.0
 
Package: synapter
Commit: 6be7c1a65b500bf5c3b072ee6550113d07757df3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-13 20:26:04
Commit message:

 add missing documentation
 
Package: synapter
Commit: 86ff056b970757724e7f1c85a47176b6446e3f96
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-13 19:54:13
Commit message:

 remove old updateSynapterObject calls
 
Package: synapter
Commit: 8754621d2e11e6774e6a921a059e24fa781d30e1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-13 19:43:24
Commit message:

 provide interface updateObject/isSynapterObjectOutOfDate
 
Package: synapter
Commit: 9763b4e660ed4b6a264368f4f1271241a2115aee
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-13 19:33:42
Commit message:

 adapt .updateSynapterObject to .isSynapterObjectOutOfDate
 
Package: synapter
Commit: d9420842e6280c0a51678d55e1250a6ea5734f8c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-13 19:32:44
Commit message:

 add .isSynapterObjectOutOfDate
 
Package: synapter
Commit: 792867dff00e0bd3d706bae362b0f1583c27e1e9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-11 21:22:32
Commit message:

 fix svn url
 
Package: synapter
Commit: 43db2b89435bfcfe2b676f83a434091592e269ea
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-11 20:46:57
Commit message:

 new devel version
 
Package: synapter
Commit: e93f535fd87e0d25b46d03c3a6f6e81cb2c48a1a
Author: l.gatto <l.gatto@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-11-11 20:46:12
Commit message:

 fix version number

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@96676 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: c1f227d336619bd5912e84f3d63885c740411856
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-11 20:21:38
Commit message:

 fix conflicts
 
Package: synapter
Commit: b78976ac39912040eccb307903d34b7cbcbae69a
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-11 20:20:51
Commit message:

 replaced with RELEASE 3.0, 1.8.1
 
Package: synapter
Commit: 6cb45d16b4f9d40acd92a18c798835b095012bef
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-11 19:22:31
Commit message:

 use MSnbase:::utils.list2ssv instead of paste
 
Package: synapter
Commit: 28b66f5ff319cf48321abbeef93eacde5b9cb96c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-11 18:58:49
Commit message:

 fix @noRd roxygen tag
 
Package: synapter
Commit: 90765856fe99ddd034ac5fd1685915b85762bdbe
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-11 18:57:49
Commit message:

 Merge branch 'fragmentLibrary' into 2.0
 
Package: synapter
Commit: 38cdc1506b22e0d20d162e09e2cd09dec9ced5ff
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-11 18:52:43
Commit message:

 add write{FragmentLibrary,MasterPeptides} methods
 
Package: synapter
Commit: e28fae157c92cd0aeec38f1f9163c5de87d5329b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-11 18:48:27
Commit message:

 store fragment library as MSnExp in master; closes #74
 
Package: synapter
Commit: f61618cc10d13309b982568cbb6f89ff9b236008
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-10 23:23:06
Commit message:

 deprecate gui and update vignette
 
Package: synapter
Commit: bc4c90224eae59b831efa4164a8e11d2c7514c89
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-08 21:44:09
Commit message:

 Merge branch 'fragmentLibrary' into 2.0
 
Package: synapter
Commit: acb677039e1be371f1af806e2e12609206ced8f8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-08 21:44:04
Commit message:

 Merge branch '3DgridSearch' into 2.0
 
Package: synapter
Commit: cc483dcfe4bcbb0e9bb1017be4b8db6ff14ce321
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-06 20:28:12
Commit message:

 regenerate precursor.leIDs in makeMaster
 
Package: synapter
Commit: 66ecdfd03dbcb4bd59ebc4dea32c8dc5e29cba04
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-06 20:05:24
Commit message:

 add .createFragmentLibrary (#63)
 
Package: synapter
Commit: 51ad6abfede0b1af5928883a6a37953d52614486
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-11-01 11:42:17
Commit message:

 replace any(is.na(...)) by anyNA(...); synapter depends on R >= 3.1.0 now
 
Package: synapter
Commit: 92e2c1d165b9678c6b60c0b381b6ffa6f550b2ff
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-13 21:47:41
Commit message:

 Bumping versions after creating 3.0 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: fd5c857eb89b58073c9d750d70f1b566eb21d3b0
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-13 21:38:33
Commit message:

 Bump package versions prior to creating the 3.0 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/synapter@95439 bc3139a8-67e5-0310-9ffc-ced21a209358
 
Package: synapter
Commit: c38c44a14bbd116af7e14408a7b737c84a24b7f1
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-09-17 15:51:47
Commit message:

 Merge branch 'master' of github.com:lgatto/synapter
 
Package: synapter
Commit: bfa9f81353fcd5ecc49fc9b33cd664d61421b1d4
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-09-17 15:51:32
Commit message:

 update biocviews
 
Package: synapter
Commit: f6f4cbc82a5b4275230d00d8a3052c9dc1415599
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-09-15 16:33:05
Commit message:

 Merge branch 'master' into 3DgridSearch
 
Package: synapter
Commit: 54c2e0d70796c73a59e0734a4e50fc8af19e5784
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-09-15 16:32:49
Commit message:

 fix sequence handling in plotCrossMatching
 
Package: synapter
Commit: f1f7a40649448f87a8c79eb0729090c805e8cbaf
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-09-15 15:10:51
Commit message:

 Merge branch 'master' into 3DgridSearch
 
Package: synapter
Commit: 851cadb28b97d8284573a936a7236a7cbb2d44cb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-09-15 15:10:38
Commit message:

 convert non-ascii characters to _
 
Package: synapter
Commit: f0b06b60d5a853e15e16fa75f766004b006cc7eb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-09-15 15:10:21
Commit message:

 filter empty fragment entries
 
Package: synapter
Commit: 2b8ee39f3dab1bca5c3c1667b41b77d90bdb5925
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-21 15:43:02
Commit message:

 set minimalVersion to 1.7.2
 
Package: synapter
Commit: d577383e5ae8708f619a8e8cd151a9dae04722a7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-21 15:25:17
Commit message:

 Merge branch 'master' into 3DgridSearch

Conflicts:
	DESCRIPTION
	NEWS
 
Package: synapter
Commit: 1936b66393a3d4adbcc2a012d5793f911fb263a2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-07-13 15:47:25
Commit message:

 fix typo
 
Package: synapter
Commit: 383a9d2be2b96361e343bf73a2adf772dc1522d9
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-05-17 21:18:58
Commit message:

 updating vignettes
 
Package: synapter
Commit: b4a84a728a76b33f61fece76486bdd00dbed5342
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-05-17 20:18:47
Commit message:

 updated crossmatching vignette
 
Package: synapter
Commit: 8049f7f4c5b72d75814b043390ce12781f97dab0
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-05-17 11:40:54
Commit message:

 some updated to crossmatching vig
 
Package: synapter
Commit: b29c52db6bcff2893490da6e7326e130b0a03493
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-05-16 22:03:03
Commit message:

 adjust version number
 
Package: synapter
Commit: 4a4f1f57cddd48bd003102baaccc46401c544572
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 16:13:57
Commit message:

 update NEWS entries
 
Package: synapter
Commit: 81a8e182487844b554757d22c400f3229432cbc5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 16:01:07
Commit message:

 turn warning about missing ion mobility into a message
 
Package: synapter
Commit: 42439aef43fb74ce8dc071a159c39b5f62e4e9b1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 15:57:13
Commit message:

 update plotGrid/plotFeatures documentation
 
Package: synapter
Commit: 35968159d957eedd53b21faab7ce9a737e46de28
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 15:46:59
Commit message:

 add documentation for {set,get}ImDiff
 
Package: synapter
Commit: ee8904d596a077afd210f47fc1be7009a25b8512
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 15:41:23
Commit message:

 export {set,get}ImDiff
 
Package: synapter
Commit: 3544f7b974f9412efcc1be7447dc6f92e67c82d5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 15:40:43
Commit message:

 test for imthreshold == Inf
 
Package: synapter
Commit: c95b2193fb5c8b7222d669be025a63fcbc694bf6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 15:03:26
Commit message:

 adapt plotFeatures(..., what = all) to 3D grid search
 
Package: synapter
Commit: 4bcc749d1896773dbf63ec81b8f1d7239caef32e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 14:52:36
Commit message:

 adapt plotGrid
 
Package: synapter
Commit: fa23d1bfbbd1a9c2a0ed3c0eac0f118b02da1d91
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 14:28:54
Commit message:

 fix spelling
 
Package: synapter
Commit: 6b59b0a22e9c3da3891609b5eea435e34cd7372a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 13:50:11
Commit message:

 fix rownames order
 
Package: synapter
Commit: 60696668983ce2482d1c3275eadca5143616e5a9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 13:35:31
Commit message:

 remove searchGrid2
 
Package: synapter
Commit: 38bbe48ada7b9cdd634b1841e2894c9885896200
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 13:34:59
Commit message:

 adapt findEMRTs
 
Package: synapter
Commit: b97790575477639f6e0d152bdd432a60cf18fbc8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 13:34:34
Commit message:

 add {set,get}ImDiff
 
Package: synapter
Commit: 98c42353718b314a2fdea79515f0d50c1f39e2fd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 12:34:09
Commit message:

 set ImDiff by setBestGridParams
 
Package: synapter
Commit: 48eec538d1a1de71a7b4d7b72da41820f67526a4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 12:26:52
Commit message:

 bump version to 1.7.4 and introducing ImDiff field to synapter class
 
Package: synapter
Commit: af49f0041394adefcce39556cf8b92cce1cda0be
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 12:09:32
Commit message:

 adapt getBestGridParams to gridSearch3
 
Package: synapter
Commit: 8ca1f8365994c015256daefe60bfa31873564e1b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 12:09:19
Commit message:

 set dimnames of grid search results
 
Package: synapter
Commit: 9b6d01a6b01364a7fe169445f15b6f72de05aa5b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 11:57:14
Commit message:

 adapt searchGrid to new gridSearch3
 
Package: synapter
Commit: a962fff30588e0d6393369ae4658b412e6ffcaeb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-16 11:13:36
Commit message:

 first implementation of a 3D grid search
 
Package: synapter
Commit: ce35e4b02dc111e0ae74f1730734f8a9845f2005
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 23:11:38
Commit message:

 set not matched ids in gridSearchResult to "no_quant_id" (#67)
 
Package: synapter
Commit: 63daee36d5499b1f8e3ba43ff21561a3c7439293
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 23:01:37
Commit message:

 rename matchType column into gridSearchResult (#67)
 
Package: synapter
Commit: b922e61721d465111ceeb225eddfc2d104430d86
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 22:25:54
Commit message:

 add crossmatching vignette
 
Package: synapter
Commit: e8816101220bbd2ec79ad7a41a9381cce7267244
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:43:52
Commit message:

 clarify flatEMRT message (#67)
 
Package: synapter
Commit: 62fbc4cb7c700b887c97e0c9c50df78319ae2ea4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:38:21
Commit message:

 add warning if .filter{Non}UniqueMatches is used multiple times
 
Package: synapter
Commit: 3d8a5bfa5454bf51487e7580b3897ff470ba195e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:37:56
Commit message:

 fix Function assignment in .filterNonUniqueMatches
 
Package: synapter
Commit: 41d84bf3d24e83c9d2ea4cb60cf2ec2e5c7d1cde
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:13:07
Commit message:

 don't remove rows in filter{Non}UniqueMatches
 
Package: synapter
Commit: 5e13369f997e816ba6db15a1426099cd3dc1b518
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:12:34
Commit message:

 use pch=1 for number of peptides == 0
 
Package: synapter
Commit: 981c5339f23fff4becc22b04fa089550e689b825
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:11:25
Commit message:

 adjust confusionMatrix calculation to new rank
 
Package: synapter
Commit: 73324a8dca7190fc1f8d66e4664916310a3fc54a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 19:09:29
Commit message:

 use rank instead of sort(..., index.return=TRUE)
 
Package: synapter
Commit: 7690f6e8c72ba6bf9a965312d48ada6901a02018
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 15:44:11
Commit message:

 filter fragment.str in .filterIntensity (filterFragments) as well
 
Package: synapter
Commit: ddb2c008ca6d8dc0787157e712d235ff22e4c7af
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-15 13:53:12
Commit message:

 remove fragment matching lines from the create-synobj2 chunk
 
Package: synapter
Commit: 9d0f931ca0f8ff47d6ce457cac3cee2905d70418
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 19:59:00
Commit message:

 adapt ion mobility vignette to new synobj2 (#66)
 
Package: synapter
Commit: 59e53e2356329b9700f456ea3054f99e46e05d0d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 19:58:05
Commit message:

 remove vignettes/Makefile
 
Package: synapter
Commit: 006b5a38ac2103e7f0fa4aac1689ecccfc60ff8f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 19:11:25
Commit message:

 replace CCP by CPU
 
Package: synapter
Commit: 02d10259d72926f9ce599a9d2c62338683829861
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 17:03:24
Commit message:

 export plotCumulativeNumberOfFragments
 
Package: synapter
Commit: 46873a0ac35e509dc03b72c142e351ee890403f4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 15:04:26
Commit message:

 Merge pull request #58 from lgatto/ionmobility

summary plot for ion mobility 
Package: synapter
Commit: ff2074ce6395d902928b008027a813473e1ff0e9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 15:01:37
Commit message:

 add NEWS entry for ion mobility vignette
 
Package: synapter
Commit: d27cf49f8438cd101ef6c68276a0600ae5faa4be
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 14:57:39
Commit message:

 add basic ion mobility vignette
 
Package: synapter
Commit: 79a754bd66b27f4df0f5496cd79cf4bdf686b153
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 14:57:08
Commit message:

 move .groundTruthIndices to ionmobility-functions.R
 
Package: synapter
Commit: af6fdc21b8e0c17ebf18ad5713326d8a9de7c626
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 13:18:28
Commit message:

 Merge branch 'master' into ionmobility

Conflicts:
	R/crossmatching-functions.R
 
Package: synapter
Commit: 61397011f9a293f904647147ac6d5b1b2046e46a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-08 20:52:12
Commit message:

 introduce filterFragments and plotCumulativeNumberOfFragments

Conflicts:
	NEWS
	R/AllGenerics.R
	R/synapter-class.R
	R/synapter-interface.R
	man/Synapter.Rd
 
Package: synapter
Commit: 3ce58612bdb4194a7f23bd8f223e3e57ad3a73e5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 09:17:51
Commit message:

 fix flatMatchedEMRTs unit test
 
Package: synapter
Commit: 0c18e6c4d8ddab3dd74d5955d71a659560f5e6a5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-14 00:35:29
Commit message:

 export filterFragments
 
Package: synapter
Commit: 5cd40d5724d712b3fae0c522e19a07ebf1af2fca
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-13 13:06:16
Commit message:

 move NEWS entry from 1.7.2 to 1.7.3
 
Package: synapter
Commit: d0d1854a90d6179721e84d3d82d62dfd89fd7a05
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-13 13:02:10
Commit message:

 reintroduce ion information for flatted MatchedEMRTs df

Conflicts:
	R/ionmobility-functions.R
 
Package: synapter
Commit: de4032eb2dbdf69f27a1dfe5fea9ad80af3f3e0b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-13 13:01:10
Commit message:

 extract ions that are used for identification (isFid == 1) from the Pep3D df instead of the first instance
 
Package: synapter
Commit: 5993bad33e811deec2abf86f4599f333b2836ce1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-13 13:02:10
Commit message:

 reintroduce ion information for flatted MatchedEMRTs df
 
Package: synapter
Commit: 965a11daf03714d7bb074348c584a3e72045f15e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-13 13:01:10
Commit message:

 extract ions that are used for identification (isFid == 1) from the Pep3D df instead of the first instance
 
Package: synapter
Commit: 63c0bd4a2adece1bd9d1193bca0627949e159081
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-11 00:20:36
Commit message:

 Remove old cx filter methods and replace them by new ones

- Removes filterMatchedEMRTsByCommonPeaks, plotCrossMatchingSummary,
  plotCrossMatchingDiff, plotCrossMatchingCumulativeNumberOfFragments.
- Changes plotCrossMatchingPerformance (replaces old plot functions by a simple
  two panel plot).
- Adds filterUniqueMatches and filterNonUniqueMatches (replaces
  filterMatchedEMRTsByCommonPeaks).
 
Package: synapter
Commit: 42a907d654e1aaea37ead217c24c3b7dac90d1fb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-09 20:05:09
Commit message:

 fix .plotCxDiff
 
Package: synapter
Commit: 2eff27d582cdeb7e0320208345e9b32e245926a4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-09 16:24:06
Commit message:

 add plotCrossMatchingDiff and diff filter
 
Package: synapter
Commit: 99b1247341e747ba54125494a41997e44a50f518
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-08 21:02:13
Commit message:

 Merge pull request #65 from lgatto/filterFragments

introduce filterFragments and plotCumulativeNumberOfFragments 
Package: synapter
Commit: 8575d9dbc641dc7a7901388f21c4eaca01200f50
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-08 20:52:12
Commit message:

 introduce filterFragments and plotCumulativeNumberOfFragments
 
Package: synapter
Commit: 9a64a0c337837176dfb1eaa27f8ffcaafa25bd53
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-06 12:50:38
Commit message:

 Merge pull request #64 from lgatto/cxPerformance

cross matching performance plots 
Package: synapter
Commit: 7a72b2781deecb635816fb5cf37be0acb10b5320
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-06 12:39:40
Commit message:

 add cx columns to MatchedEMRTs data.frame

Adds the columns "spectrum.identXfragments.quant",
"spectrum.quantXfragments.ident" and "fragments.identXfragments.quant" to the
MatchedEMRTs data.frame.
 
Package: synapter
Commit: 92efca4b9b955798b8e4e1f7df333f33fb664462
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-06 11:56:55
Commit message:

 add plotCrossMatchingPerformance
 
Package: synapter
Commit: fef18b4e09bda45de96ead42a9b026fefdbb7b60
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-06 10:57:25
Commit message:

 add "what" argument to cross match filter

Adds a "what" argument to filterMatchedEMRTsUsingCrossMatching. This argument
could be `c("non-unique", "all")`. For "all" all rows that are not matching the
criteria are remove from the MatchedEMRTs data.frame. "non-unique" just turns
non unique matches into unique ones, without removing anything.
 
Package: synapter
Commit: 45f15b8d66973d95a5bc60c44f3cd74c61f82214
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-05 16:11:35
Commit message:

 throw warning if the user already filtered by CX

Throws a warning if the column "Function.0" is already present in the
CrossMatching data.frame to show the user that he won't get the expected results
if he runs filterMatchedEMRTsUsingCrossMatching multiple times on the same
synapter object.
 
Package: synapter
Commit: 8a63322a2021db0ee2279d43d595252d37148c9c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-02 12:43:51
Commit message:

 set .self to span if it is given as argument to modelRt
 
Package: synapter
Commit: 773a16120a6d931abd065d684a4a1152fd51f01c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-02 09:46:47
Commit message:

 add argument equalCharge

Add argument equalCharge to compare only the ion mobility of equally charged
ions. The correct way would be to go back to the pep3d file and fetch the ion
mobility for the corresponding charge state from there. But because the current
results are not satisfying it seems to be not worth the additional effort.
 
Package: synapter
Commit: e6862845eb6160aa6266ef89e7329e492b96c513
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-05-01 18:43:03
Commit message:

 remove PLGS digestion

Remove the PLGS argument for `dbUniquePeptideSet` introduced in
https://github.com/lgatto/synapter/pull/57. It was full of bugs (some per
purpose some not) and a waste of time!

Now the default cleaver rules are used (again).
 
Package: synapter
Commit: 0396025f86476d8d2430c39ed4f327e9e4210cc9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 21:21:18
Commit message:

 Merge pull request #61 from lgatto/IL

add argument ILequal to dbUniquePeptideSet; closes #60 
Package: synapter
Commit: 188c903f00dc3c67cdb844f1dcc01325898b9ef2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 17:53:47
Commit message:

 add missing IisL argument
 
Package: synapter
Commit: bcf3b5e049d471886cfea7454637ccce66b74501
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 17:12:43
Commit message:

 Merge pull request #62 from lgatto/removePrecursor

add removePrecursor/tolerance argument to load{SpectrumXml,FragmentCsv}Files 
Package: synapter
Commit: 57ae3ace67750e3025dbbc8f88c7f7f17a0e8325
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 16:47:31
Commit message:

 Merge branch 'removePrecursor' into IL

Conflicts:
	NEWS
 
Package: synapter
Commit: 198ded19b512e8f3f7dad5425ae9c7cb87aa895b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 13:52:36
Commit message:

 add removePrecursor/tolerance argument to load{SpectrumXml,FragmentCsv}Files; closes #59
 
Package: synapter
Commit: 9e26f8ba8761fde5fe874b89bdb108c1e5c11ad3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 14:14:11
Commit message:

 change IisL default to FALSE (same behaviour as synapter < 1.7.3)
 
Package: synapter
Commit: 463f6cb0719fa779b2dc429255d60b611e405885
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 14:05:35
Commit message:

 Revert "remove default value for IisL argument"

This reverts commit 579fb7223140377ae597cd3cfde22715390b0d6f.
 
Package: synapter
Commit: ac9906a2d4e09c3983b61a4997402cdb6cc4fdde
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 13:32:17
Commit message:

 fix missedCleavages > 1 for PLGS rule
 
Package: synapter
Commit: 579fb7223140377ae597cd3cfde22715390b0d6f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 13:28:02
Commit message:

 remove default value for IisL argument
 
Package: synapter
Commit: a445ccbee8fbbebfa3c1a0c75ebde0d4f5a3b9f1
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 11:22:06
Commit message:

 rename ILequal into IisL
 
Package: synapter
Commit: a09fd563e919ba402c94a1356ca70d1069633a42
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 11:00:08
Commit message:

 extend verbose output of dbUniquePeptideSet
 
Package: synapter
Commit: 5d028e9449444abeda4df2933a5dbb599456cd7f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-30 09:45:46
Commit message:

 add argument ILequal to dbUniquePeptideSet; closes #60
 
Package: synapter
Commit: daeb8ebdbd196c29c224421146551fb854a06b96
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 18:10:35
Commit message:

 bump version number (the NEWS file already contains entries for 1.7.3)
 
Package: synapter
Commit: eb1e0ed4f6743d06cb7c6f796f11b74e62884d25
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 17:50:40
Commit message:

 move logic of filterUnique{Ident,Quant}DbPeptides into filterUniqueDbPeptides and call dbUniquePeptideSet only once; closes #55
 
Package: synapter
Commit: c63003db0d7505be5efa3714379eb93cbf168096
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 17:39:38
Commit message:

 throw a warning if PLGS/missedCleavage settings are differ between current and RDS
 
Package: synapter
Commit: 63ea6e43b39dc78ae9c81e6f7475bb50c94b2a63
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 17:21:54
Commit message:

 add PLGS argument to estimateMasterFdr
 
Package: synapter
Commit: a5c5f756bad7e652683195852df33865248265d7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 17:05:24
Commit message:

 hide fasta digest/rds loading in dbUniquePeptideSet interface
 
Package: synapter
Commit: a9eeee00a9e01d00edb7cbdeb7693504e3b2e3a8
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 16:57:18
Commit message:

 add createUniquePeptideDbRds (regards #55)
 
Package: synapter
Commit: e2c0d57d9b1c369fe4541c1a42ba95dde2e91eba
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 16:32:59
Commit message:

 return cleavage results as vector
 
Package: synapter
Commit: 6eae079387da547feea6b136c592cb8d6a2d116b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 16:13:48
Commit message:

 Merge pull request #57 from lgatto/missedCleavages

emulate PLGS' peptide cleavage; close #53 
Package: synapter
Commit: 4a9b2b916f6c4119bb4dfada6eb22819f0b5a9f7
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 14:48:16
Commit message:

 add .plotIonMobilitySummary
 
Package: synapter
Commit: 85e0893884401e5beba2cfc1819c797e94bd723c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 13:54:36
Commit message:

 move groundTruthIndices to utils.R
 
Package: synapter
Commit: eecc2d5bc835bbdf0671f21b9abbff712724ae33
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-29 13:37:28
Commit message:

 add PLGS argument to dbUniquePeptideSet
 
Package: synapter
Commit: d01398906257e3ebfe79e0a10a3dfaa879250516
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 21:15:30
Commit message:

 reduce number of cleavages in step 4
 
Package: synapter
Commit: 7c796077ab1d640950c99d60fed29eeadde3ef84
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 20:51:57
Commit message:

 emulate PLGS' peptide cleavage; close #53
 
Package: synapter
Commit: ca5b2a48ac478c605317af9282b054b2dc144d02
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 19:57:31
Commit message:

 Merge pull request #56 from sgibb/fragmentmatching

fragment matching 
Package: synapter
Commit: 0997a87c1f2e872ba18cd2cd6a740816180f03fb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 16:05:27
Commit message:

 Merge remote-tracking branch 'upstream/master' into fragmentmatching

Conflicts:
	NEWS
	R/figures.R
 
Package: synapter
Commit: a05a841e13ee88df19768096969bb43888b46414
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 16:03:24
Commit message:

 add matchColumn argument to filterMatchedEMRTsByCommonPeaks and plotCrossMatchingSummary
 
Package: synapter
Commit: 38e6586d39c36d71ac89a485c568f96427e27e9b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 15:29:52
Commit message:

 fix rt model calculation in plot.some.features
 
Package: synapter
Commit: b5c72a7d3bd7f02f837d203952effea64d26945a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-28 09:03:06
Commit message:

 rename load{Spectra,Fragments} into load{SpectrumXml,FragmentCsv}Files
 
Package: synapter
Commit: 60f582d08934c947a14245d52bca4e75cb2712ce
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 22:29:41
Commit message:

 fix handling of multiple non unique matches after applying common peaks threshold
 
Package: synapter
Commit: 86f4d7f845696df615901e4b5576ffa7b4b5d1f9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 22:28:21
Commit message:

 remove useless spaces
 
Package: synapter
Commit: 90c527408fae35152f8a0f14aeb27f843fd8ba3e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 22:27:58
Commit message:

 convert number of minimal common peaks to integer + typo
 
Package: synapter
Commit: 76cf1a5e488e67bb9927db44da46c246703ef9ea
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 13:58:43
Commit message:

 export crossMatching
 
Package: synapter
Commit: d13d256e5a42f8735f648a0e21af15020a66bc7b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 12:54:11
Commit message:

 move cross matching functions from spectrum-functions.R to crossmatching-functions.R
 
Package: synapter
Commit: 7a100236592fc7a475d16e0f7b8c7cc8ab46d0aa
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 12:50:07
Commit message:

 add filterMatchedEMRTsByCommonPeaks
 
Package: synapter
Commit: 949cd8c13acd36d91e0d63c154ee3f563e70d5bd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 12:17:13
Commit message:

 add testthat to Suggests
 
Package: synapter
Commit: 8103f88e44c26685a8eee0b192cee549b38946be
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 12:16:31
Commit message:

 fix crossreferences
 
Package: synapter
Commit: 21f95d897d9d7c691c64b3a4a50b33f81a2ccb86
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 10:39:44
Commit message:

 add {set,get}CrossMatchingMinimalNumberOfCommonPeaks
 
Package: synapter
Commit: d3486d0852a68dc1d636bc0a841983163e0bb9a2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 10:18:08
Commit message:

 replace plotCrossMatching{Fdr,Boxplots} by plotCrossMatchingSummary
 
Package: synapter
Commit: d2f7fa8af1b5caf2dc428dd3a75452a0d4f78663
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 09:10:24
Commit message:

 call updateSynapterObject automatically in loadSpectrum/loadFragments
 
Package: synapter
Commit: 4fb3f863e2e9ad3c858240d357354f97e3ae287b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 08:30:30
Commit message:

 refine plotCrossMatchingFdr documentation
 
Package: synapter
Commit: 8310e873c007085ba9cae59fc526030852ec233d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-25 08:20:41
Commit message:

 use %in% instead of ==
 
Package: synapter
Commit: bb6129cd5d58d74c282fb560689c686f98a37c8e
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-24 19:24:41
Commit message:

 add grid to plotCrossMatchingFdr
 
Package: synapter
Commit: 2b29eb6dba2370edd7fb554974fce7de0185e808
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-24 18:59:12
Commit message:

 replace plotCrossMatchingNonUniqueDiff by plotCrossMatchingBoxplots
 
Package: synapter
Commit: 606320b28d85934a48b16d12f2a937a89fdf3ea4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-04-24 18:12:46
Commit message:

 add .filterMatchedEMRTsUsingCrossMatching
 

Source Code & Build Reports »

Source code is stored in Git.

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:

Developer Resources: