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commit 4dfbc01c1ec656fed8e0d3a4e262193f1061ebb3
Author: jotsetung <[email protected]>
Date:   Fri May 26 11:52:55 2017 +0200

    Fix issue #180

commit 8dfccd382b73c3f772b4a80b7d2fbe38b57c0a96
Author: jotsetung <[email protected]>
Date:   Fri May 26 08:56:17 2017 +0200

    Update NEWS.

commit d290cbeb8d57a69305f7f7315135fa26f6eb80b5
Merge: 56c43dd d2d4b7a
Author: jotsetung <[email protected]>
Date:   Thu May 25 17:17:59 2017 +0200

    Merge branch 'devel' into xcms3

commit d2d4b7a2a18a9a1620eaa52e94dc81edb2c939e9
Merge: f11aac4 d9baa6c
Author: Johannes Rainer <[email protected]>
Date:   Thu May 25 16:31:59 2017 +0200

    Merge pull request #178 from stanstrup/patch-4

    scanrange was collapsed when the adjusted range was reported.

commit d9baa6ca364f4dd197a9eedd361869cf0787dbc3
Author: Jan Stanstrup <[email protected]>
Date:   Mon May 22 14:01:47 2017 +0200

    scanrange was collapsed when the adjusted range was reported.

    ```r
    > scanrange=c(1,1400)
    > message("Provided scanrange was adjusted to ", scanrange)
    Provided scanrange was adjusted to 11400
    >
    >
    > message("Provided scanrange was adjusted to ", scanrange[1]," - ", scanrange[2])
    Provided scanrange was adjusted to 1 - 1400
    >
    ```

commit 56c43ddfd7eece4fe58f1f81da66714bf23e32ef
Author: jotsetung <[email protected]>
Date:   Fri May 19 12:20:29 2017 +0200

    Fix for issue #173

    - Stitching of mzML files did not fill in mz and intensity values for the last
      spectrum.

commit 95a8deadbc29b7433678cd35b05690961c99dd6c
Author: jotsetung <[email protected]>
Date:   Thu May 18 15:36:54 2017 +0200

    Fix for issue #175

    - Disable original xcms-preprocessing vignette.

commit 36535df5d03137a1d3db62fbf7a9f85c7fdaf8a9
Author: jotsetung <[email protected]>
Date:   Mon May 15 09:08:31 2017 +0200

    Add extractMsData method (issue #120)

    - Add extractMsData to extract MS data (mz, rt, intensity duples) as a
      data.frame (related to issue #120).
    - Add related unit tests and documentation.

commit b273693c627451f470d1c5a91c435f384ce9cdf7
Author: jotsetung <[email protected]>
Date:   Fri May 5 13:21:14 2017 +0200

    Fix for bug introduced into plotChromPeakDensity

commit ad6aa2bf4bec129147c1407d0325f531dcf1fcb0
Author: jotsetung <[email protected]>
Date:   Fri May 5 13:03:00 2017 +0200

    Add Jan Stanstrup's fix also to the plotChromPeakDensity function

commit 906be43e92aee5ac54b97ee795ada7848cbae5c5
Author: jotsetung <[email protected]>
Date:   Fri May 5 13:00:30 2017 +0200

    Update news.

commit 11ed73c97b5c1ea28354172da7f639eff85bae38
Merge: e90b74e f11aac4
Author: jotsetung <[email protected]>
Date:   Fri May 5 12:59:04 2017 +0200

    Merge branch 'devel' into xcms3

commit f11aac4020319d991b845154e492f1031f946888
Author: jotsetung <[email protected]>
Date:   Fri May 5 12:43:06 2017 +0200

    Fix problem with merge from Jan Stanstrup

    - Remove definitions of argument n in density functions other than in
      do_groupChromPeaks_density: fixes errors in the vignette.
    - Fix issue #161.

commit 9129650cdba019bcacba62441d2623e50168a498
Merge: 77c51a4 60ff595
Author: Johannes Rainer <[email protected]>
Date:   Fri May 5 11:14:26 2017 +0200

    Merge pull request #162 from stanstrup/patch-5

    fixes for #161: increase parameter `n` in `density` function calls for *peak density* correspondence.

commit e90b74e3c30bdf3860b475b549db6fdb158ecd60
Author: jotsetung <[email protected]>
Date:   Fri May 5 11:10:57 2017 +0200

    Remove un-needed functions from functions-XCMSnExp.R

commit 77c51a444c14b962c54b3ca6c0eabc7dd3f7c2f8
Merge: 14e701c cf3a862
Author: Steffen Neumann <[email protected]>
Date:   Fri May 5 09:49:28 2017 +0200

    Merge branch 'biocdevel' into devel

commit 58e35e588c0f4654f013f06933356b0d232f1f99
Author: jotsetung <[email protected]>
Date:   Fri May 5 09:41:03 2017 +0200

    Add plotChromPeakDensity function (issue #171)

    - Add the plotChromPeakDensity function to evaluate peak density correspondence
      settings.
    - Add related unit tests and documentation.

commit 9de2927231f6c92fe600381ec5f3758093dd642d
Author: jotsetung <[email protected]>
Date:   Tue May 2 09:32:25 2017 +0200

    Add new clean,Chromatogram method

    - Add new clean,Chromatogram method.
    - Add related unit tests and documentation.

commit f7719b8d4c8a04cc2bc349802c309441e3fee382
Author: jotsetung <[email protected]>
Date:   Thu Apr 27 22:18:33 2017 +0200

    Fixes to the extractChromatograms method

    - Ensure that the returned lists per rt/mz range have the same lengths than
      there are files.
    - Return a Chromatogram object of length equal to the number of scans within the
      specified retention time range, even if no measurement is available for the
      provided mz range (report NA_real_).
    - Add parameter missing to the extractChromatograms method to allow specifying
      the intensity value to be used if no signal was measured for a rt in the
      specified mz range.

commit 20c7e9e048d8117733f8af7309307308262ee563
Author: jotsetung <[email protected]>
Date:   Wed Apr 26 08:12:47 2017 +0200

    extractChromatograms extracts multiple ranges

    - extractChromatograms extracts multiple ranges to enable efficient chromatogram
      extraction without re-reading the raw data (issue #168).
    - Add corresponding unit tests and documentation.
    - Fix in plotChromatogram to avoid warnings if the number of measured data
      values differs between files (issue #167).
    - Extend new_functionality vignette.
    - Disable parallel processing in preprocessing vignette.

commit cf3a86263557c2856b67e707075ee26079525d71
Author: [email protected] <[email protected]@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Apr 24 19:50:57 2017 +0000

    bump x.y.z versions to odd y after creation of 3_5 branch

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 93322452e483ec8e98ea5a85dfca261557822e06
Author: [email protected] <[email protected]@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Apr 24 19:25:24 2017 +0000

    bump x.y.z versions to even y prior to creation of 3_5 branch

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 77b0396c54e2afe61de1df09271ec1ce427781e3
Author: jotsetung <[email protected]>
Date:   Fri Apr 21 15:25:27 2017 +0200

    Fix bug in plotChromatogram

commit 612cecfc868a55b94c43cf01d16b15ea6c56418c
Author: jotsetung <[email protected]>
Date:   Fri Apr 21 14:27:48 2017 +0200

    Ensure plotChromatogram doesn't break if no data available

commit af6eea822cb9edb1d9d979289617b022b6947584
Author: jotsetung <[email protected]>
Date:   Fri Apr 21 09:20:35 2017 +0200

    Add plotChromatogram and highlightChromPeaks functions

    - Add plotChromatogram and highlightChromPeaks functions (issue #167).
    - Add documentation.

commit d045d708e1802f81e54a307220d19e0b18253a61
Author: jotsetung <[email protected]>
Date:   Wed Apr 19 09:57:22 2017 +0200

    Fix validation method for CentWaveParam if roiList is provided

commit 14e701ce3e3c0f271bb7f6f38a678f132d007442
Merge: f775cbb 84a5375
Author: Steffen Neumann <[email protected]>
Date:   Fri Apr 14 19:20:26 2017 +0200

    Merge branch 'biocdevel' into devel

commit 84a537533db6a5f399ff350888f5e8e964867e62
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Fri Apr 14 17:19:30 2017 +0000

    Squashed commit of the following:

    commit f775cbb7336e160ff7157d5e897c5cd1a0e93d8c
    Merge: aa9f1d3 30bb9b2
    Author: jotsetung <[email protected]>
    Date:   Thu Apr 13 18:59:42 2017 +0200

        Merge branch 'xcms3' into devel

    commit 30bb9b270ff90a4a54b8e752f3abf8dd609ee811
    Author: jotsetung <[email protected]>
    Date:   Thu Apr 13 18:57:46 2017 +0200

        Update date

    commit 9d507248152612eabc049cd887f838aa525545d9
    Author: jotsetung <[email protected]>
    Date:   Thu Apr 13 13:22:42 2017 +0200

        Avoid fillPeaks using deprecated API (issue #163)

        - Implement .getPeaks_new that does no longer depend on deprecated profFun
          calls.
        - Change getPeaks to use by default the new .getPeaks_new function (fixes
          fillPeaks issue #163).
        - Add corresponding unit tests.

    commit 0b26f47f3bb48080c5691af82631e176e6312018
    Author: jotsetung <[email protected]>
    Date:   Mon Apr 10 08:24:36 2017 +0200

        Fix possible memory problem in obiwarp (issue #159)

        - Fix issue #159.
        - Add example on how to inspect raw peak data in the new user interface (issue
          #155).

    commit a7cc281eae4013c691afacccaf010596756266b6
    Author: jotsetung <[email protected]>
    Date:   Fri Apr 7 08:06:22 2017 +0200

        Update documentation of fillPeaks.chrom

        - Update the documentation of fillPeaks.chrom.
        - Display message if nSlaves is used suggesting to use BPPARAM instead (issue
          #158).

    commit 00786dab2f8d73ad9fdf45f17da28d8f024fe89c
    Author: jotsetung <[email protected]>
    Date:   Thu Apr 6 08:04:07 2017 +0200

        Clean up imports and dependencies

        - Import specific functions from Biobase instead of the full package.
        - Move packages from Depends to Imports.

    commit e4a970e93d8a1c14baf920684bfae5e2f9ea91cd
    Author: jotsetung <[email protected]>
    Date:   Wed Apr 5 06:29:26 2017 +0200

        Add parameters mz, rt, ppm and type to chromPeaks (issue #156)

        - Add parameters mz, rt, ppm and type to the chromPeaks method to enable
          extracting chromatographic peaks from the specified range(s).
        - Add related documentation and unit tests.
        - Documentation tidying.

    commit 7fcc690bbc484805528151e26434cd806d244ce4
    Author: jotsetung <[email protected]>
    Date:   Tue Apr 4 16:56:34 2017 +0200

        Add parameter "filled" to featureValues

        - Add parameter filled to the featureValues,XCMSnExp method (issue #157).
        - Add related unit tests and documentation.

    commit aa9f1d3e5241cc22c7ade7165c168bdfb6399e8d
    Merge: 828883b ecbe9a7
    Author: Steffen Neumann <[email protected]>
    Date:   Fri Mar 31 13:58:31 2017 +0200

        Merge branch 'biocdevel' into devel

    commit 828883b412f7973f10eacbd58eac2744500ecb13
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 31 07:50:44 2017 +0200

        Updates to the vignette

    commit cbe41fac512d7ed267b3d1a36bccb023fe776615
    Author: jotsetung <[email protected]>
    Date:   Thu Mar 30 13:03:59 2017 +0200

        Add the plotAdjustedRtime function (issue #141)

        - Add the plotAdjustedRtime function to visualize alignment results (issue #141)
        - Add corresponding documentation, unit tests and examples.
        - Code tidying.
        - Include plotAdjustedRtime to vignette.

    commit 592ecdc097dfa72fc92027df46133144d387394b
    Author: jotsetung <[email protected]>
    Date:   Thu Mar 30 09:02:12 2017 +0200

        Support predefined peak group matrix for peak groups alignment

        - Support peak groups-based alignment using a pre-defined peak groups
          matrix (issue #153).
        - Add related unit tests and update documentation.

    commit 985c051ebdd6a7c7f9fe86c19b0616e32458e2c1
    Author: jotsetung <[email protected]>
    Date:   Wed Mar 29 22:01:07 2017 +0200

        Add peakGroupsMatrix slot to PeakGroupsParam class

        - Add peakGroupsMatrix slot to the PeakGroupsParam class (issue #153).
        - Add related unit test and update documentation.

    commit 2ec98ddfef91ebaf5e9f10d51cc44b94647e4dbb
    Author: jotsetung <[email protected]>
    Date:   Wed Mar 29 14:38:15 2017 +0200

        Remove private 'isSeizmo' massifquant function.

        - Remove the private isSeizmo function from massifquant's C++ code (issue #149).

    commit 0b97c0d38ab8a874a25ce260adbd5c0631898a9b
    Author: jotsetung <[email protected]>
    Date:   Tue Mar 21 09:53:00 2017 +0100

        Add adjustRtimePeakGroups function (issue #147)

        - Add adjustRtimePeakGroups function for XCMSnExp that returns the peak groups
          that would be used for a given PeakGroupsParam parameter object.
        - Add related documentation and unit tests.

    commit 59f1f4940517517f5b3aa324d1ce55ee2c45541a
    Author: jotsetung <[email protected]>
    Date:   Mon Mar 20 17:23:16 2017 +0100

        Use feature IDs as rownames in featureValues and featureDefinitions

        - Add arbitrary feature IDs as rownames to the featureDefinitions DataFrame and
          use these also for the matrix returned by featureValues (issue #148).
        - Add related documentation and unit tests.

    commit 6b52f86e267846e637411fbaddc5e6271230ef81
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 17 16:25:03 2017 +0100

        Add filterRt,Chromatogram method

        - Add a filterRt,Chromatogram method (issue #142).
        - Add related unit tests and documentation.

    commit 0e0a9909d3f684a923c4454b4e64d2dc9a8d8aad
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 17 15:21:13 2017 +0100

        Ensure correct ordering of values in Chromatogram constructor

        o Order intensity and retention time values by retention time if not
         increasingly ordered in the Chromatogram constructor (issue #145).

    commit d2f3d141558585e5df094d64876b84f1a8749666
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 17 08:06:52 2017 +0100

        Change order of alignment and correspondence in XCMSnExp,show

    commit f8148d567b9e2f406755f27149334a103f0b23b4
    Author: jotsetung <[email protected]>
    Date:   Wed Mar 15 16:22:03 2017 +0100

        Fix unordered adjusted retention times in peakGroups

        o Fix adjustRtime,XCMSnExp,PeakGroupsParam to return for some data adjusted
          retention times that are not in the same order than raw retention times
          (issue #146).

    commit c697bfd54397f856207769ce28a7b75794402379
    Author: jotsetung <[email protected]>
    Date:   Wed Mar 15 09:15:54 2017 +0100

        Ensure adjusted and raw retention times to be in the same order

        o For adjustRtime,XCMSnExp,PeakGroupParam ensure that adjusted retention times
          are in the same order than the raw retention times (issue #146).
        o Show warning if adjusted retention times have to be re-adjusted accordingly.
        o Show warning if adjusted retention times are not ordered.

    commit 2b66b28e3905618f7543a6b4b44176ca6bbebf6d
    Merge: b4c4885 dfe23f3
    Author: jotsetung <[email protected]>
    Date:   Tue Mar 14 15:53:49 2017 +0100

        Merge branch 'devel' into xcms3

    commit b4c48850e6976bc599fc02bb5d224bd69ae370b6
    Author: jotsetung <[email protected]>
    Date:   Tue Mar 14 15:52:07 2017 +0100

        Show warning if order of adjusted retention time is not increasing

        o Show a warning message if the adjusted retention times for a file are not
          ordered increasingly (issue #146)

    commit dfe23f315235d0ac965b712de2cd995f54204ec0
    Merge: ed89456 215409c
    Author: Steffen Neumann <[email protected]>
    Date:   Fri Mar 10 23:09:00 2017 +0100

        Merge branch 'biocdevel' into devel

    commit e8dbb4c094b0cbaa6a962320047f941f52474207
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 10 22:02:31 2017 +0100

        Avoid multiple/nested parallel processing

        - Avoid multiple/nested parallel processing calls (issue #144).
        - Documentation update with newer roxygen2 package.

    commit ed8945662d82612911bcdbf4be3333ea750d1ef6
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 10 11:12:53 2017 +0100

        Change default backend for mzML files to pwiz (issue #143)

    commit cf6b1bca8d966a9bc2ffc34d68bfedb76c4eeb93
    Author: jotsetung <[email protected]>
    Date:   Thu Mar 9 17:04:16 2017 +0100

        Remove debug centWave version debug message

    commit e9f39ecd6540aae7ba4a438d9ca8b26a1e8e80ff
    Author: jotsetung <[email protected]>
    Date:   Wed Mar 8 08:44:30 2017 +0100

        Extend new_functionality vignette.

    commit 572f2ebe0d840929dc4db7fb671f9a54016f7861
    Author: jotsetung <[email protected]>
    Date:   Tue Mar 7 12:51:15 2017 +0100

        Add fillChromPeaks for matchedFilter peak detection

        o Add support for matchedFilter identified peak in
          fillChromPeaks,XCMSnExp (issue #130).
        o Add related documentation and unit tests.

    commit 6af52f4458663c40fba939044ce5f24c9c8de49c
    Author: jotsetung <[email protected]>
    Date:   Mon Mar 6 14:35:01 2017 +0100

        Remove commented old matchedFilter test functions.

    commit e899b923086b8c540f26a0b1fdb468eb0cd701a3
    Author: jotsetung <[email protected]>
    Date:   Mon Mar 6 13:43:58 2017 +0100

        Ensure XCMSnExp compatibility for single spectrum MS data

        o Check XCMSnExp on single spectrum direct injection MS data (issue #106).
        o Add related unit tests.

    commit 5c6454c1f53da31e898c393a3181465229726e8a
    Author: jotsetung <[email protected]>
    Date:   Mon Mar 6 12:27:36 2017 +0100

        Support peak filling for direct infusion data

        o Add support for MSW identified peaks of single spectra, direct infusion data
          in fillChromPeaks,XCMSnExp.
        o Add documentation and related unit tests.

    commit 889caf0f3ba0188646868d493ee0ba6dc3d9d9bb
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 3 13:58:52 2017 +0100

        Extend show method for XCMSnExp

    commit c9c061fd76e883d33431830a4277d721678af060
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 3 13:36:52 2017 +0100

        Fix expand.rt and expand.mz in fillPeaks (issue #139)

    commit e51387f7cc7ec952ad258b4b9bd6d46897e582e3
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 3 13:09:54 2017 +0100

        Add featureValues method for XCMSnExp

        o Add featureValues method for XCMSnExp (issue #131).
        o Add related unit tests and documentations.

    commit f7c0547dc6b422d8980b159710a56e4debc04be5
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 3 12:26:31 2017 +0100

        Add dropFilledChromPeaks method

        o Add dropFilledChromPeaks method (issue #140).
        o Add related documentation and unit tests.

    commit e48e977a2e50943e8d41d011515e985362014768
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 3 10:41:43 2017 +0100

        Add @filled slot for XCMSnExp to xcmsSet conversion

    commit 083fd4b2594ae8e5703ca04ca527ff6a12453fa4
    Author: jotsetung <[email protected]>
    Date:   Fri Mar 3 10:35:40 2017 +0100

        Add fillChromPeaks method and FillChromPeaksParam class

        o Add fillChromPeaks method and FillChromPeaksParam class.
        o Add related unit tests and documentation.

    commit b1b430239a2c5e4e7dda3777e442535f474f5ead
    Author: jotsetung <[email protected]>
    Date:   Thu Mar 2 13:12:28 2017 +0100

        o Remove debug messages from xcmsSet.

    commit d469000b45403204e8796dd1de0dd07fabf7e32c
    Author: jotsetung <[email protected]>
    Date:   Wed Mar 1 15:26:33 2017 +0100

        Add modified centWave function and various fixes

        o Add modified centWave function that integrates peak intensity using only
          signal within the peak area (issue #136).
        o Fix error in findChromPeaks if no peaks were found (issue #137).
        o Fix for failing unit test checking break definition functions (issue #118).

    commit c821b33adea47101f8e4044ddc3e66b11764665f
    Merge: 8e44a7b e4b4f89
    Author: jotsetung <[email protected]>
    Date:   Mon Feb 27 22:11:31 2017 +0100

        Merge branch 'devel' into xcms3

    commit 8e44a7bb32b532da9fc86c07a7676c1223a6acd5
    Author: jotsetung <[email protected]>
    Date:   Mon Feb 27 18:47:34 2017 +0100

        Update NEWS

    commit 2d670e210408e778cd896553632e0e9b3969b0ac
    Author: jotsetung <[email protected]>
    Date:   Sun Feb 26 22:12:49 2017 +0100

        Fix for issues #118 #133 #134

        o Disable part of failing unit test for issue #118 - try to reproduce on a
          windows build machine
        o issue #134: show information message if no files are provided showing the
          directory in which files are listed and the number of found files.
        o issue #133: don't re-index samlples if no peaks were identified.

    commit e4b4f8951ae599f3764d29372c23d3dbcc64cd57
    Merge: 861e938 d421682
    Author: Steffen Neumann <[email protected]>
    Date:   Fri Feb 24 22:12:22 2017 +0100

        Merge branch 'biocdevel' into devel

    commit 78a98b1e8c2612a847382ff741da49a90786c6c0
    Author: jotsetung <[email protected]>
    Date:   Fri Feb 24 08:38:39 2017 +0100

        Add columne "is_filled" to chromPeaks matrix

    commit 1743262d1d03865461bc489bf76fc0a566608f4e
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 23 18:58:44 2017 +0100

        Add findChromPeaks for XCMSnExp objects (issue #128)

    commit 8068dbeb2d955121179c6974b94c6aa7d7b0d610
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 23 13:26:21 2017 +0100

        Rename parentMz in Chromatogram to precursorMz

        o Rename Chromatogram class slot parentMz into precursorMz to fit with the IUPAC
          definition.

    commit b358862912447e017ad9b9406cbe369abc357aae
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 23 08:02:13 2017 +0100

        spectra,XCMSnExp returning adjusted rtime (issue #129)

        o spectra,XCMSnExp returns adjusted rtime within the Spectrum objects, if such
          retention times are present in the XCMSnExp object.
        o Add related documentation and unit tests.

    commit 861e93805afcf2da1add7adfde71e403333c8fe0
    Author: jotsetung <[email protected]>
    Date:   Wed Feb 22 11:06:19 2017 +0100

        Fix issue #127: failing unit test on tokay2 build machine

    commit 2ae5eafdebe4c225d3a1de7b194a89093507d109
    Author: jotsetung <[email protected]>
    Date:   Wed Feb 22 10:52:34 2017 +0100

        Rename methods, functions and objects (issue #126)

        o Rename most of the methods from the new user interface to follow a common
          nomenclature.

    commit 009e57a15b6a2969d460144bec30b2b098485377
    Author: jotsetung <[email protected]>
    Date:   Wed Feb 15 09:39:04 2017 +0000

        Ensure memory cleanup in parallel findPeaks for xcmsSet

    commit 6da82fc146eb80e3058ce56cfe2bc536818fce82
    Author: jotsetung <[email protected]>
    Date:   Wed Feb 8 12:15:02 2017 +0100

        Minor changes to Chromatogram

        o Don't export Chromatogram.

    commit c4bca930c1f897e1fe3b3db6c01cfb6f7c456d27
    Author: jotsetung <[email protected]>
    Date:   Mon Feb 6 08:27:36 2017 +0100

        Add Chromatogram class

        o Add Chromatogram class (related to issue #120).
        o Add methods, unit tests and documentation.

    commit f6e169fbfbfe9ac9ee83d6677317def6b2714b8a
    Merge: b0deb92 84eee36
    Author: Steffen Neumann <[email protected]>
    Date:   Fri Feb 3 09:59:01 2017 +0100

        Merge branch 'biocdevel' into devel

    commit b0deb92a9b8df81fe7b2ea6e2129ae46bc282cfa
    Author: jotsetung <[email protected]>
    Date:   Fri Feb 3 09:20:54 2017 +0100

        Bump version and update NEWS.

    commit 70040008b630ede4a8c5ff569fce27bf798a4616
    Author: jotsetung <[email protected]>
    Date:   Fri Feb 3 08:40:41 2017 +0100

        Fix issue #124

        o Fix issue #124: filterRt,XCMSnExp returns empty object.
        o Extend unit tests for above fix.

    commit 2f1add71e4440547b006c5534ba10328f8f8feef
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 18:48:02 2017 +0100

        Bump version.

    commit 0c9b416ea9128ecbbce3ce567a71d7462b776cdb
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 18:45:06 2017 +0100

        Small internal changes.

    commit 09eb5e3f5e784157e8b50e159cef9c05cf725bc8
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 15:21:15 2017 +0100

        Small code cleanup.

    commit 00fd415e0b14070b3bf9a417283b98a9a888c065
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 15:01:58 2017 +0100

        Update NEWS.

    commit 806d79351a46d5369d2e056010ca33f6d7c5d5f4
    Merge: 2d2ecf8 6e0381e
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 14:48:35 2017 +0100

        Merge branch 'devel' into xcms3

    commit 2d2ecf85d66ce24309499c60834448694ac5eb60
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 14:18:48 2017 +0100

        Fix unit test error on R-3.2.3

    commit 7720ea5c0de35552ca8c25e782e1e9df7ab47023
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 12:20:49 2017 +0100

        filterRt filtering by default on adjusted rt if available

        o Fix filterRt to filter on adjusted retention times if available.
        o Fix filterRt to filter features correctly for adjusted = FALSE.
        o Extend unit tests to ensure proper functionality.
        o Extend documentation.

    commit 7aeee29b3eaddceae9ba613083162b0a5066b6c7
    Author: jotsetung <[email protected]>
    Date:   Thu Feb 2 07:28:23 2017 +0100

        rtime,XCMSnExp reports by default adjusted rt

        o rtime,XCMSnExp method reports by default, if present, adjusted retention
          times (issue #123).
        o Add/fix related unit tests and adapt documentation.
        o Extend other documentations.

    commit 079836e67c1bb607759bd51e17edee66230cfb3a
    Author: jotsetung <[email protected]>
    Date:   Wed Feb 1 10:54:21 2017 +0100

        Add groupval,XCMSnExp method (issue #114)

        o Add the groupval,XCMSnExp method.
        o Add documentation and unit tests.

    commit 359ad1c2492c0c3b334de29297465284b3eaa226
    Author: jotsetung <[email protected]>
    Date:   Wed Feb 1 06:25:58 2017 +0100

        Add adjustRtime,XCMSnExp,ObiwarpParam (issue #119)

        o Add adjustRtime obiwarp alignment for XCMSnExp and OnDiskMSnExp.
        o Add documentation and unit tests.

    commit d4ceb5f5fbae010575cf76f7ffffe130093639d3
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 30 09:10:53 2017 +0100

        Tentative fix for issue #118

        o Using checkEquals instead of checkIdentical on the failing unit test.

    commit d6df84b9c3ab052fc20d7591fb9d4a39de4db793
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 30 09:05:51 2017 +0100

        Add ObiwarpParam class (issue #119)

        o Add the ObiwarpParam class.
        o Add related documentation and unit tests.

    commit 940fecdcc931cdc83b0011b6299b56affc3e5e98
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 27 06:56:51 2017 +0100

        Implement profMat method for XCMSnExp and OnDiskMSnExp

        o Implement the profMat method for OnDiskMSnExp and XCMSnExp objects (issue
          #115).
        o Add related documentation and unit tests.

    commit 98b53f3ceff0b26c2ff9afc091cba73a8705442f
    Author: jotsetung <[email protected]>
    Date:   Wed Jan 25 14:59:47 2017 +0100

        Use do_adjustRtime_featureGroups in retcor.peakgroups

        o Modify the retcor.peakgroups method to use the do_adjustRtime_featureGroups to
          perform the retention time correction (issue #111 and #112).
        o Add related unit test to compare to the original code.

    commit 4a2d9659ba665e0d3a5f032257666a703846db5f
    Author: jotsetung <[email protected]>
    Date:   Wed Jan 25 13:45:03 2017 +0100

        Add adjustRtime,XCMSnExp,FeatureGroupsParam method

        o Add the retention time adjustment equivalent to retcor.peakgroups (issue
          #112).
        o Add related unit tests and documentation.
        o Enhance and fix the dropFeatures, dropFeatureGroups and dropAdjustedRtime
          methods and the features<-, featureGroups<- and adjustedRtime<- methods (see
          issue #113).
        o Add related documentation and unit tests.

    commit 569dff0f2a4148e04f0d2a83419d0b0f858ecbbe
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 24 15:06:07 2017 +0100

        Add FeatureGroupsParam object (issue #112)

        o Add FeatureGroupsParam object.
        o Add related unit tests and documentation.

    commit 1f866da1b7f80d91e35f16ca4b1ab055d3c2cc3e
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 24 12:54:05 2017 +0100

        Add documentation and unit test for do_adjustRtime_featureGroups

        o Add documentation and unit test for do_adjustRtime_featureGroups (issue #111).

    commit 27c382a2d9ed436a8071b38bebed7d24703568e7
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 24 12:18:08 2017 +0100

        Amend ordering of peak goups in retcor.peakgroups (issue #110)

    commit 5d602d2185665c9feac159dacda58fdbaa36bfed
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 24 09:18:34 2017 +0100

        Add the do_adjustRtime_featureGroups function

        o The do_adjustRtime_featureGroups function performs retention time correction
          with the peakgroups method. Issue #111.

    commit 6c005cf0ea4346a124569a0e79015a6722136b8a
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 16:26:56 2017 +0100

        Remove commented code.

    commit 9b88134182343a19992fe99100d39c0c62b9242b
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 16:13:21 2017 +0100

        Add groupFeatures,XCMSnExp,NearestFeatures method (issue #108)

        o Add the groupFeatures,XCMSnExp,NearestFeatures method.
        o Add related unit tests and documentation.

    commit 73311ba4e6b4417f48d00a327168e2b5c47c3ca0
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 15:32:50 2017 +0100

        Add NearestFeaturesParam class (issue #108)

        o Add the NearestFeaturesParam class with all methods and functions.
        o Add related documentation and unit tests.

    commit dde4b3a9d585c33bc91c2705b696e53a2a73d21d
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 13:15:36 2017 +0100

        Fix warnings in group.nearest (issue #109)

    commit ec0daf60ed1c6d01e696dc7e927c25d10b651912
    Merge: 8fd3010 8312b64
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 11:10:29 2017 +0100

        Merge branch 'xcms3' of https://github.com/sneumann/xcms into xcms3

    commit 8fd301034eefa35e87dbbccb47aec86643e79297
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 10:38:28 2017 +0100

        Add do_groupFeatures_nearest function (issue #103)

        o Add the do_groupFeatures_nearest function.
        o Add unit tests and documentation.

    commit 8312b6469d37fc923c0cd6ac6bc1a17bcd4eec59
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 20 10:38:28 2017 +0100

        Add do_groupFeatures_nearest function (issue #103)

        o Add the do_groupFeatures_nearest function.
        o Add unit tests and documentation.

    commit 848b6c21d1fcd6bab86a669c78de1a3a3594d445
    Author: jotsetung <[email protected]>
    Date:   Thu Jan 19 16:02:03 2017 +0100

        Add groupFeatures,XCMSnExp,MzClustParam (issue #107)

        o Add groupFeatures,XCMSnExp,MzClustParam method.
        o Add documentation and unit tests.

    commit 8f4230089e538631d87bc30b45c0b1c5a640e474
    Author: jotsetung <[email protected]>
    Date:   Thu Jan 19 14:43:22 2017 +0100

        Add MzClustParam class and smaller bug fixes

        o Add the MzClustParam class along with all required methods (issue #107).
        o Add unit tests and documentation.
        o Add support for R-3.2.3: fix problems with S4Vectors and sort method.

    commit a98f9fb67ec76eb9cc6905533f50b9e60f9a65c4
    Author: jotsetung <[email protected]>
    Date:   Wed Jan 18 16:13:45 2017 +0100

        Fix order issue (issue #180 in MSnbase)

        o Remove argument 'method' from any calls to order to ensure backward
          compatibility.

    commit 5c11a30aeef599220a8a87188fb8e50552beb19f
    Author: jotsetung <[email protected]>
    Date:   Wed Jan 18 06:55:23 2017 +0100

        Add do_groupFeatures_mzClust function (issue #103)

        o Add the do_groupFeatures_mzClust function.
        o Add unit tests and documentation.

    commit 797ec556f78cb3e241a8bccd90f06c615126170d
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 17 15:53:54 2017 +0100

        Add groupFeatures,XCMSnExp,FeatureDensityParam method

        o Add the groupFeatures,XCMSnExp,FeatureDensityParam method to perform the
          feature alignment using the density method (issue #105).
        o Add unit test and documentation.

    commit 900c1d14f6343c2da8f3cf7515e8c77d9ac0bf0c
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 17 14:06:35 2017 +0100

        Add FeatureDensityParam class (issue #105)

        o Add the FeatureDensityParam class, all related methods and functions.
        o Unit tests and documentations for FeatureDensityParam.

    commit bb2f22a0f092d99527dde11c7c8fc99145979d6b
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 17 11:01:24 2017 +0100

        Parallel version of the do_groupFeatures_density implemented

        o Function implemented but not exported - no performance increase with the
          parallel version.

    commit 458b9e353ea184d861d21e27ce08fcefe300cce9
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 17 10:19:10 2017 +0100

        Replace code in group.density with do_groupFeatures_density (#103)

    commit 9edb01c2d9986d15d48d65ce95ed00edc86901bc
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 17 09:22:08 2017 +0100

        Add do_groupFeatures_density function

        o Add the first feature alignment core API function: do_groupFeatures_density:
          issue #103.
        o Add unit tests and documentation.

    commit 6e0381eef656d2f32fa8d3affabd2a9f995bfc38
    Merge: 87a57f1 283023b
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Jan 17 08:28:38 2017 +0100

        Bump version and adapt NEWS

    commit 87a57f1c4d1ab4da77093dc529ed4def9b1bc0e2
    Merge: 5e288f4 62452c2
    Author: Steffen Neumann <[email protected]>
    Date:   Mon Jan 16 22:57:21 2017 +0100

        Merge remote-tracking branch 'origin/xcms3' into devel

    commit 5e288f41000a7aab07e2b0e4cc61232fb7baa1f3
    Merge: a4421c3 4c6815a
    Author: Steffen Neumann <[email protected]>
    Date:   Mon Jan 16 22:57:07 2017 +0100

        Merge branch 'biocdevel' into devel

    commit 62452c2b5204f515e57579aaa8c614173c44750b
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 16 12:57:22 2017 +0100

        Removed , in DESCRIPTION

    commit bdc3d65b646447f4b7fef7ba650623d2bcacb87f
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 13 21:28:54 2017 +0100

        Add spectrum,XCMSnExp method and increase method robustness

        o Add spectrum,XCMSnExp method to extract spectra grouped by samples (bySample
          parameter). Issue #96.
        o Ensure robustness of methods with a bySample parameter: the returned list has
          always the same length as there are files, with elements being empty if no
          e.g. mz values are present for a specific file (because it got e.g. filtered).

    commit d8e9a21f1ed58e0167e68164c2b98f48e0f826fb
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 13 13:33:54 2017 +0100

        Fix issue #102

    commit 95f5c30fdd727e0419de928553121d204e032ae4
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 13 13:29:26 2017 +0100

        Fix issue #91.

        o Replay the changes made by Jan Stanstrup.

    commit 839fdb369875f895c06d627dedbe5161e3600f2c
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 13 13:17:31 2017 +0100

        Fix issue #98

        o Fix error in flagme vignette. Ensure that number of rows of the profile matrix
          is equivalent to what produced in the old code. Problem was that previously
          the mzrange of the xcmsRaw object was altered, i.e. represented rounded *real*
          mz range. The number of rows in the profile matrix were then equal to the
          length of the sequence seq(mzrange[1], mzrange[2], by = step). The new code
          however always ensures that the real max mz value is included, i.e. it
          produces one more bin in cases were in the old approach the max mz would have
          been floored (new code: always do ceiling).

    commit c602fef616c8060b196c00f933fe22c6ee289394
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 13 08:01:13 2017 +0100

        Add bySample parameter to features,XCMSnExp

        o Add the bySample parameter to the features,XCMSnExp method allowing to extract
          the feature matrices grouped by sample.

    commit f7053990d515702911850aa400908f4e5d7c5b14
    Author: jotsetung <[email protected]>
    Date:   Thu Jan 12 16:21:50 2017 +0100

        Fix for the last improvement of the issue #99 fix.

    commit 223798c30f8852d3c4696f4284facbe4152a08c8
    Author: jotsetung <[email protected]>
    Date:   Thu Jan 12 07:58:19 2017 +0100

        Update NEWS.

    commit 277324fec07683db2b08e09c0077ce243f9d327f
    Author: jotsetung <[email protected]>
    Date:   Thu Jan 12 07:53:47 2017 +0100

        Improve fix for issue #99

        o Only throw an error if the rtrange is completely outside the available rt.

    commit 707990ee9ae0f27e8d7e7fd3b5c8e6ef6048db90
    Author: jotsetung <[email protected]>
    Date:   Wed Jan 11 08:28:01 2017 +0100

        Method to coerce XCMSnExp to xcmsSet

        o Add setAs method to coerce XCMSnExp to xcmsSet (issue #100).
        o Add related unit tests and documentation.
        o Add examples for XCMSnExp usage.

    commit 9419493c8dda575dd6e74417e62d2c3a62989394
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 10 16:10:47 2017 +0100

        Fix issue #101

        o Fix the xcmsRaw function to not copy over MSn data if msleve = 1 is provided.

    commit 804e8bca6f6322b42ffa88467b1ff2e45038a819
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 10 09:15:50 2017 +0100

        Add filterRt method for XCMSnExp

        o Implement the filterRt method for XCMSnExp objects that allows to filter the
          object by retention time. Subsets also features, featureGroups and adjusted
          retention time. Issue #96.

    commit 0bcb852e280294f0d58e016d69f1ad02c6368bbd
    Merge: 48055c0 7962641
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 9 16:01:17 2017 +0100

        Merge remote-tracking branch 'refs/remotes/origin/xcms3' into xcms3

    commit 48055c072e5589fa2fd3351b5a14de0b5bbc3a9b
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 9 08:16:42 2017 +0100

        Add bySample argument to adjustedRtime,XCMSnExp method

        o Add the bySample argument to the adjustedRtime,XCMSnExp method.

    commit 79626414dd15957ebec9d47c1dc18ccba9b85dab
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 9 08:16:42 2017 +0100

        Add bySample argument to adjustedRtime,XCMSnExp method

        o Add the bySample argument to the adjustedRtime,XCMSnExp method.

    commit 2e30a970c7e091bfdd575397985cfe1d985d0cca
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 9 06:52:03 2017 +0100

        Add mz, intensity and rtime methods for XCMSnExp

        o Add mz, intensity and rtime methods for XCMSnExp objects extending the
          corresponding methods for OnDiskMSnExp by adding the bySample parameter.

    commit 4aa10f595f103f2f8a7ef9b080a4407b3a41dd3a
    Author: jotsetung <[email protected]>
    Date:   Fri Jan 6 22:24:13 2017 +0100

        Use drop* methods to remove preprocessing results

        o Use the drop* methods to remove preprocessing results from XCMSnExp objects.

    commit 8f1fc5cba7ea93c47ff60bdc76a5799693d09249
    Author: jotsetung <[email protected]>
    Date:   Tue Jan 3 18:29:41 2017 +0100

        Add sort method option

        o Add sort method option that defaults to "auto" on R versions < 3.3. See
          https://github.com/lgatto/MSnbase/issues/180 for more info.

    commit 6ae59333718b341ce3b40ec74b4e83007e975ed4
    Author: jotsetung <[email protected]>
    Date:   Mon Jan 2 21:22:48 2017 +0100

        Fix failed execution of unit tests

    commit a1122065a96cf6e69088417d82fe987cda188cd5
    Author: jotsetung <[email protected]>
    Date:   Fri Dec 30 21:57:02 2016 +0100

        Add drop methods

        o Add dropFeatures, dropFeatureGroups and dropAdjustedRtime for XCMSnExp and
          MsFeatureData objects to remove the corresponding results.
        o Remove obsolete Rd files.

    commit 477f0db3fd58f0aedef21e06d062b2f19e86f5c2
    Merge: e92a02d a4421c3
    Author: jotsetung <[email protected]>
    Date:   Sun Dec 25 18:49:49 2016 +0100

        Merge branch 'devel' into xcms3

    commit e92a02d2b0bb24bb9c58b615879f430fa35a9b61
    Author: jotsetung <[email protected]>
    Date:   Fri Dec 23 15:27:37 2016 +0100

        Implement filterMz method for XCMSnExp

        o Add the filterMz method for XCMSnExp that allows filtering on an mz value
          range. features and featureGroups are retained if they are completely within
          the mz range. Adjusted retention time is not altered.
        o Add unit tests and documnentation.

    commit 6dec3689c906b8557ebfe3bee91c1592e22852a2
    Author: jotsetung <[email protected]>
    Date:   Fri Dec 23 14:04:37 2016 +0100

        Fix problem reading MS2-only files.

        o Fix issue https://github.com/MassBank/RMassBank/issues/174

    commit 9c9319da5bd9be139648680805fb59d175a4abea
    Author: jotsetung <[email protected]>
    Date:   Fri Dec 23 12:29:03 2016 +0100

        Implement some of the methods inherited from OnDiskMSnExp

        o Implement all data manipulation methods from OnDiskMSnExp for XCMSnExp
          class (issue #96). All drop xcms pre-processing results.
        o Implement filterFile for XCMSnExp, does subset identified features.
        o Add documentation and unit tests.

    commit a4421c35caef0aaee129a222c128c99c25b218a5
    Merge: 62932b7 1ddbb89
    Author: Steffen Neumann <[email protected]>
    Date:   Fri Dec 23 12:01:16 2016 +0100

        Merge branch 'devel' of github.com:sneumann/xcms into devel

    commit 62932b77c7407c04ed0d49bbe7d7ad2cf82371f0
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Fri Dec 23 11:00:28 2016 +0000

        added deepCopy to avoid corrupting the original object, thanks to J. Stanstrup, closes #93

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125419 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit 2ab8350f93056ba300eee06b7ef14212bd65ceaf
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Fri Dec 23 11:00:19 2016 +0000

        added deepCopy to avoid corrupting the original object

        #76

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125418 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit 832f67adc75df88264aa017361788f2b2632da91
    Author: jotsetung <[email protected]>
    Date:   Fri Dec 23 06:37:34 2016 +0100

        Code cleanup

        o Comment unneeded (mostly testing purpose only) functions.
        o Remove previously commented out functions and code.
        o Add xcms startup message.

    commit c0ac4b7c622ccb211fcbb526a649e05ec514536f
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 22 16:22:15 2016 +0100

        Extend show method for XCMSnExp objects.

    commit a58cf39f9ebde3e6dc3ee94795fd3cb9addb18e5
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 22 15:23:36 2016 +0100

        Enable XCMSnExp as return object in detectFeatures

        o Return the XCMSnExp object as a result object from the detectFeatures method.
        o Add related unit tests and update documentation.
        o XCMSnExp is ready to run (issue #85).

    commit 46c27495d87083dd41890e9ec2663f3ae669ef3d
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 22 13:38:19 2016 +0100

        Export the ProcessHistory and XProcessHistory classes

        o Export the ProcessHistory and XProcessHistory classes allowing to keep track
          of performed data analysis steps.
        o Add the processHistory method for XCMSnExp objects.
        o Add unit tests and documentations.

    commit 1fbf8b525a7557239c24296c62b4d98b9860e226
    Author: jotsetung <[email protected]>
    Date:   Wed Dec 21 21:45:45 2016 +0100

        Implement the detectFeatures method for CentWavePredIsoParam

        o Implement the detectFeatures method for CentWavePredIsoParam class.
        o Add documentation and unit tests.

    commit a3324552b94599b38995f117e9f3ce860465d83a
    Author: jotsetung <[email protected]>
    Date:   Wed Dec 21 16:34:47 2016 +0100

        Add rtime,XCMSnExp method

        o Add rtime,XCMSnExp method that returns the retention time grouped per sample.

    commit f5f7d04610e4d1aeb2cbbd4b4315f89568317b66
    Author: jotsetung <[email protected]>
    Date:   Wed Dec 21 15:48:09 2016 +0100

        Add XCMSnExp class

        o Add the XCMSnExp class and export the MsFeatureData class (issue #85).
        o Add methods hasAdjustedRtime, hasAlignedFeatures, hasDetectedFeatures,
          features, features<-, featureGroups, featureGroups<-, adjustedRtime,
          adjustedRtime<-.
        o Add unit tests and documentation.

    commit cb148d5da0527462b548f0da04274ed8b505764c
    Author: jotsetung <[email protected]>
    Date:   Wed Dec 21 12:20:15 2016 +0100

        Add MsFeatureData class

        o Add the MsFeatureData class for storing xcms preprocessing results (see issue
          #85 and https://github.com/lgatto/MSnbase/issues/177).
        o Add unit tests and validity function for the new object.

    commit 1ddbb890ddb2e5d741571c79647821c6d96c14a6
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 20 22:14:46 2016 +0100

        added deepCopy to avoid corrupting the original object, thanks to J. Stanstrup, closes #93

    commit 37280ef115738daccd392c10f9e4b4fe5f6543a6
    Merge: 5160700 fef11aa
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 20 21:43:15 2016 +0100

        Merge branch 'stanstrup-patch-3' into devel

    commit fef11aac12ca51f227ac9302fe960997563e11a3
    Merge: 5160700 ba80552
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 20 21:43:02 2016 +0100

        Merge branch 'patch-3' of git://github.com/stanstrup/xcms into stanstrup-patch-3

    commit 5160700df8728f54c4460a0054ba975b05662f05
    Merge: 8b595bf 647e2f9
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 20 21:41:28 2016 +0100

        Merge branch 'devel' of github.com:sneumann/xcms into devel

    commit 8b595bf187e6f97de4d19508c7faab73062ad593
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Tue Dec 20 20:39:30 2016 +0000

        adapted manpage for plotQC

        From: Steffen Neumann <[email protected]>

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125356 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit b95b7689e622b50e55f76c2caaf19c25e6071c32
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Tue Dec 20 20:39:20 2016 +0000

        merged xcms3 branch, added return value to plotQC()

        From: Steffen Neumann <[email protected]>

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125355 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit 647e2f9c5fc7e6ea40d839c9846b07d668a95f0d
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 20 21:34:30 2016 +0100

        adapted manpage for plotQC

    commit cf29b17d73c32bb0b89f7b7166fcb9cf9decec1e
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 20 21:32:50 2016 +0100

        merged xcms3 branch, added return value to plotQC()

    commit ba805525dda98a90d9dd4682fbbdd0318bbab01d
    Author: Jan Stanstrup <[email protected]>
    Date:   Tue Dec 13 11:34:53 2016 +0100

        added deepCopy to avoid corrupting the original object

        #76

    commit dde6cba65156aedd28c36be89e64944d4e4e3389
    Merge: d771f06 3385098
    Author: jotsetung <[email protected]>
    Date:   Tue Dec 13 11:26:02 2016 +0100

        Merge branch 'devel' into xcms3

    commit 33850986e49365cbbdab5a0cffce65378db8ed35
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Tue Dec 13 10:14:49 2016 +0000

        do not error if a centWave ROI contains no data, closes #90

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125062 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit bc99d3d47fb913a9ae13525b88186f1209fc08ae
    Merge: 58c2ad2 ba781a1
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Tue Dec 13 10:14:41 2016 +0000

        Merge branch 'stanstrup-patch-2'

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125061 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit ba781a1ba412e303fbd36673baf1e078495e0362
    Merge: 58c2ad2 cba193b
    Author: Steffen Neumann <[email protected]>
    Date:   Tue Dec 13 11:11:47 2016 +0100

        Merge branch 'patch-2' of git://github.com/stanstrup/xcms into stanstrup-patch-2

    commit 58c2ad22057adfe1d4c7da5d06ffa75e1309a70e
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Tue Dec 13 09:52:50 2016 +0000

        Merge fix and bump version

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125060 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit 99b0eee8ca8ac60542c28065e3125cce20e09458
    Merge: 2bf72a8 02444fd
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Tue Dec 13 09:52:13 2016 +0000

        Merge remote-tracking branch 'sneumann/devel'

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125059 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit d771f06e483f8d579ba918e4b5fa56834f53d02f
    Author: jotsetung <[email protected]>
    Date:   Tue Dec 13 08:16:05 2016 +0100

        Add CentWavePredIsoParam class

        o Add CentWavePredIsoParam class, documentation and unit tests.

    commit 515b8141ab02e3726cdc52cdb69f130a5ef9f689
    Author: jotsetung <[email protected]>
    Date:   Mon Dec 12 15:24:55 2016 +0100

        Add centWaveWithPresIsoROIs core API function

        o Add do_detectFeatures_centWaveWithPredIsoROIs function (issue #82, #35).
        o Change the findPeaks.addPredictedIsotopeFeatures and findPeals.centWaveWith...
          to use the new do_ function.
        o Unit test to compare original implementation with the new one.

    commit 3232b82c34254459f2d71d0a4c7a0b8e970ad641
    Merge: 0d9d13e 02444fd
    Author: jotsetung <[email protected]>
    Date:   Sun Dec 11 19:21:14 2016 +0100

        Merge branch 'devel' into xcms3

    commit 02444fdc4f3e2264d7ff85e7320e9df955969379
    Author: jotsetung <[email protected]>
    Date:   Sun Dec 11 19:04:11 2016 +0100

        Fix wrong sample indexing in getEIC,xcmsSet

        o Fix the wrong sample indexing in getEIC,xcmsSet: issue #92.

    commit 0d9d13ec4fe9e9d0b24a4530297d436fe61b56a6
    Author: jotsetung <[email protected]>
    Date:   Sat Dec 10 22:19:13 2016 +0100

        Start implementing the do function for withAddIsotopes

    commit cba193bdeac458b978628c66d02a9dfdef69e1c6
    Author: Jan Stanstrup <[email protected]>
    Date:   Fri Dec 9 11:05:45 2016 +0100

        More informative warning.

    commit 9dc277bfeebd257b967645e61fb817c732ce16a3
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 8 12:24:43 2016 +0100

        change profStepPad to use new binning functions

        o change profStepPad, used in retcor.obiwarp, to use new binning functions.
        o Ensure consistent naming of data types for parameters in roxygen
          documentation.

    commit 94b2b7f3048cd5e944b62631ea99ee772df78e00
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 8 09:51:28 2016 +0100

        Update new_functionality vignette to new BiocStyle

        o Update the new_functionality vignette to correctly use the BiocStyle package.
        o Add the xcms.org org-file representing the future vignette describing xcms3
          in detail.

    commit fd47069e84bc2b4f519b27db9d566f42cbdb9952
    Author: jotsetung <[email protected]>
    Date:   Mon Dec 5 15:58:54 2016 +0100

        Finish unit test tuning

        o Reduce processing time in the remaining unit tests.

    commit cb382f6bf4c20a568903ad549e3d9e72146d6ea7
    Author: jotsetung <[email protected]>
    Date:   Fri Dec 2 12:57:45 2016 +0100

        Unit test tuning

        o Tuning some more unit tests.
        o Disable the benchmarking vignette.

    commit 9fdf8a952bccabe19153d98b5371f5eabd8608a2
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 1 16:23:08 2016 +0100

        Fix vignettes and tune unit tests

        o Disable parallel processing for R CMD check.
        o Fix BiocStyle templates in the new vignettes.
        o Tune unit tests and examples.

    commit 88322830e22aa9ce19749fbd1b7f40703fe22743
    Merge: cd9165b bf142bc
    Author: Johannes Rainer <[email protected]>
    Date:   Thu Dec 1 14:43:15 2016 +0100

        Merge pull request #88 from Treutler/xcms3

        implemented function "do_predictIsotopeROIs" (issue #82)

    commit bf142bc4db56af7d66a06e2caee165147ae6ed9c
    Author: Treutler <[email protected]>
    Date:   Thu Dec 1 14:03:40 2016 +0100

        split the functionality of "findPeaks.addPredictedIsotopeFeatures" / "findPeaks.centWaveWithPredictedIsotopeROIs" and implemented function "do_predictIsotopeROIs"

    commit cd9165bac43e205ffd3391ffa64aac7f42c5dac1
    Author: jotsetung <[email protected]>
    Date:   Thu Dec 1 11:21:49 2016 +0100

        Add MSW detectFeatures method

        o Add the detectFeatures,xxMSnExp,MSWParam method (issue #87).
        o Add documentation for massifquant detectFeatures method (issue #84).
        o Update NEWS.

    commit 8ace0ea8ddeefe383017920cac2a7316108473a5
    Author: jotsetung <[email protected]>
    Date:   Wed Nov 30 14:53:49 2016 +0100

        Add massifquant detectFeatures method

        o Implement the MassifquantParam class and the detectFeatures method (issue
          #84).
        o Implement the MSWParam class (issue #87).

    commit 35b3b7e476d918d7836ac6317bedb5c4ec92f60f
    Author: jotsetung <[email protected]>
    Date:   Mon Nov 28 14:59:09 2016 +0100

        Add XProcessHistory class

        o The XProcessHistory class extends the ProcessHistory class and allows to add
          a Param class to the @param slot with the settings of the processing step.
        o Notes and ideas of the new XCMSnSet object.

    commit ccecc8f3bc62ffd0245f3a23b2f3a6e85c833b9d
    Author: jotsetung <[email protected]>
    Date:   Sun Nov 27 18:44:50 2016 +0100

        Just some comments

    commit dd8cbd3c8f5aaa6e8633f7aee5185f4df009d9d4
    Author: jotsetung <[email protected]>
    Date:   Sun Nov 27 08:34:34 2016 +0100

        Add MassifquantParam class

        o Add a MassifquantParam class (issue #84).

    commit a6bfa83e3d5cce6dbfc4ce9416aaff873275d4ca
    Author: jotsetung <[email protected]>
    Date:   Fri Nov 25 11:52:56 2016 +0100

        Add warning if data is not in centroid mode for centWave

    commit 284408213e7c410e2a09e68697c737524851ed03
    Author: jotsetung <[email protected]>
    Date:   Fri Nov 25 11:32:37 2016 +0100

        Add documentation for detectFeatures centWave and matchedFilter

        o Complete the missing documentation for the parameter classes and methods and
          the detectFeature methods (issue #83).

    commit 5b1e7a261f9b69dcb79792fdb83ee02807b73589
    Author: jotsetung <[email protected]>
    Date:   Fri Nov 25 10:06:47 2016 +0100

        Implement MatchedFilterParam and detectFeatures method

        o Add the MatchedFilterParam class and related methods.
        o Implement the detectFeatures,MSnExp,MatchedFilterParam and
          detectFeatures,OnDiskMSnExp,MatchedFilterParam methods (issue #83)
        o Add related unit tests.

    commit c4990197c14f30f40278e8c29f3e443574800ee7
    Author: jotsetung <[email protected]>
    Date:   Thu Nov 24 10:38:38 2016 +0100

        Add detectFeatures method for MSnExp and OnDiskMSnExp objects

        o Implement detectFeatures,MSnExp,CentWaveParam and
          detectFeatures,OnDiskMSnExp,CentWaveParam methods to perform feature detection
          using centWave on MSnExp and OnDiskMSnExp objects from the MSnbase
          package (issue #79).
        o Add unit tests evaluating correct processing.
        o Add roiList parameter validation to CentWaveParam class.

    commit e464617e26015c18f53303226e678adb9e70299b
    Author: jotsetung <[email protected]>
    Date:   Thu Nov 17 12:33:46 2016 +0100

        Add CentWaveParam class (issue #78)

        o Add a Param and CentWaveParam class to pave the road for the feature detection
          framework.

    commit 27cf041f62238cf4e81a193e2b5f622724557c3a
    Author: jotsetung <[email protected]>
    Date:   Mon Nov 7 11:02:49 2016 +0100

        Fix remaining unit test errors

        o Fix all unit test errors due to profBin function deprecation and new
          getEIC method (issue #68).
        o Add additional unit tests to ensure getXcmsRaw and [ subsetting works
          also along with specifying scanrange.

    commit ddc4e6f571bb9ed06d3bc54c93fc102ccf67c90f
    Author: jotsetung <[email protected]>
    Date:   Fri Oct 28 19:34:26 2016 +0200

        Update getEIC method

        o getEIC method uses now the new binning and linear interpolation
          functions (issue #74).

    commit 348a598f05dd99d5fa4452a93aec4a9620453133
    Author: jotsetung <[email protected]>
    Date:   Thu Oct 27 10:47:16 2016 +0200

        Fix warnings in specDist

        o Fix warnings in specDist method (issue #73).

    commit b7cd5c9f919779100f2a6fa044835ee82e28d012
    Author: jotsetung <[email protected]>
    Date:   Thu Oct 27 08:56:50 2016 +0200

        Fix subsetting and profile matrix generation issues

        o Fix scanrange subsetting in xcmsRaw function (issue #69).
        o Avoid duplicated profile matrix generation in xcmsRaw function issue #72.
        o Add profMat method (issue #71).
        o Fix profStep<- and profMethod<- to avoid profile matrix generation
          when not needed.

    commit a98067ade4b5e03997f8c04d2897fe99391bd73f
    Author: jotsetung <[email protected]>
    Date:   Mon Oct 24 16:13:57 2016 +0200

        Deprecate old binning functions.

        o Deprecate the profBin, profBinM, profBinLin, profBinLinM,
          profBinLinBase and profBinLinBaseM functions.

    commit 0ba4586a16b142fa10992b9c929051c5f1f21b93
    Author: jotsetung <[email protected]>
    Date:   Mon Oct 24 08:03:08 2016 +0200

        Change data import to newer mzR methods

        + Use `header` and `peaks` methods from mzR for data import instead of
          un-exported private methods.
        + Fix issue #67: add argument dropEmptyScans in readRawData to emulate
          the _old_ behaviour to discard empty scans.
        + Update new_functionality.Rmd.

    commit 93c216f8269868d13ddf824d55b4eef1c4f6a1e0
    Author: jotsetung <[email protected]>
    Date:   Fri Oct 21 09:26:36 2016 +0200

        Update the new_functionality.Rmd vignette.

    commit 31139f05c72360f84ed7aec20b7a19efadf81928
    Merge: fa2fb9b fa4a97f
    Author: jotsetung <[email protected]>
    Date:   Fri Oct 21 09:20:17 2016 +0200

        Merge branch 'devel' into xcms3

    commit fa2fb9b054e06bfa4fb25ca8ac1eeb1286b77137
    Author: jotsetung <[email protected]>
    Date:   Fri Oct 21 09:04:26 2016 +0200

        Use official mzR methods for data import

        o Remove use of private ::: methods from mzR for data import and use the
          official 'header' and 'peaks' methods (issue #65).
        o Fix issue #66.

    commit b800586682acc62b63edb8954ad885f06fe434a4
    Author: jotsetung <[email protected]>
    Date:   Thu Oct 20 11:19:39 2016 +0200

        Change matchedFilter to use new binning code

        o Change findPeaks.matchedFilter and do_detectFeatures_matchedFilter to
          use the new binning code that performs the binning on the full
          matrix. This relates and fixes issues #47 and #52.
        o Change default in useOriginalCode to FALSE.

    commit 0036470d847cda9d1370194835a3748d5f2acab3
    Author: jotsetung <[email protected]>
    Date:   Thu Oct 20 06:59:38 2016 +0200

        Update findPeaks.centWave to use the do_ function

        o Update findPeaks.centWave to use the do_detectFeatures_centWave
          function.
        o Fix subsetting by scanrange in centWave (issue #64).

    commit 9611dae1e9689d67cbbfba2ceb1b5d215b921adc
    Author: jotsetung <[email protected]>
    Date:   Wed Oct 19 15:13:12 2016 +0200

        Fix scanrange parameter in findPeaks methods

        o Fix problems with the scanrange parameter in findPeaks methods:
          - findPeaks.massifquant: parameter was ignored (issue #61).
          - findPeaks.matchedFilter: parameter was partially ignored (issue
            #63).
          - findPeaks.centWave: spectra were sub-setted, but @scantime
            not (issue #64).

    commit fa4a97f903ad8dba16cad0b3247f25d85dc27d93
    Author: [email protected] <[email protected]@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Mon Oct 17 19:10:43 2016 +0000

        bump x.y.z versions to odd 'y' after creation of 3_4 branch

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit 1f816d946ed079f95dc4efa4e0aaa7cca360ef64
    Author: [email protected] <[email protected]@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Mon Oct 17 18:45:06 2016 +0000

        bump x.y.z versions to even 'y' prior to creation of 3_4 branch

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit baf28d1d1b3d9a32f20a485e5867b40369c73723
    Author: jotsetung <[email protected]>
    Date:   Wed Sep 28 09:41:16 2016 +0200

        Update the do_detectFeatures_centWave function

        o Update the do_detectFeatures_centWave function to the latest code.
        o Fix a bug in the [ method for xcmsRaw.

    commit 8a65c66a1d535603cf1b6f584099c7a0d06eda1b
    Author: jotsetung <[email protected]>
    Date:   Tue Sep 27 08:21:56 2016 +0200

        Fix issue #60

        o Fix issue #60.
        o Add documentation for do_detectFeatures_massifquant.

    commit 50848696d4fdfdd5f6c81f2c12f3e8d8e7f4bfb0
    Merge: f82432a 4b2458e
    Author: jotsetung <[email protected]>
    Date:   Tue Sep 27 06:36:00 2016 +0200

        Merge branch 'devel' into xcms3

        o Fix conflicts in methods-xcmsRaw.R and NEWS.

    commit 4b2458e54e11a874fd5a0ce42cfb4d4e475a2865
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Mon Sep 26 14:28:09 2016 +0000

        Bump version and add NEWS on documentation fixes

        git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@121387 bc3139a8-67e5-0310-9ffc-ced21a209358

    commit 87c0eb5ffac14b74133d4a3a84e18e78ee9a4bf3
    Merge: 0574910 39e1823
    Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
    Date:   Mon Sep 26 14:28:01 2016 +0000

        Merge branch 'Treutler-dev…
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26 changes: 15 additions & 11 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: xcms
Version: 1.51.4
Date: 2017-01-16
Version: 2.99.1
Date: 2017-05-10
Title: LC/MS and GC/MS Data Analysis
Author: Colin A. Smith <[email protected]>,
Ralf Tautenhahn <[email protected]>,
Expand All @@ -12,19 +12,19 @@ Maintainer: Steffen Neumann <[email protected]>
Depends:
R (>= 2.14.0),
methods,
Biobase,
BiocParallel (>= 1.8.0),
MSnbase (>= 2.1.10)
Imports:
mzR (>= 1.1.6),
BiocGenerics,
ProtGenerics,
Biobase,
MSnbase (>= 2.1.4)
Imports:
lattice,
RColorBrewer,
plyr,
RANN,
multtest,
MassSpecWavelet (>= 1.5.2),
BiocParallel,
S4Vectors
Suggests:
BiocStyle,
Expand All @@ -45,23 +45,26 @@ URL: http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms
VignetteBuilder: knitr
BugReports: https://github.com/sneumann/xcms/issues/new
biocViews: MassSpectrometry, Metabolomics
RoxygenNote: 5.0.1
Collate:
RoxygenNote: 6.0.1
Collate:
'AllGenerics.R'
'DataClasses.R'
'Deprecated.R'
'MPI.R'
'c.R'
'cwTools.R'
'databases.R'
'functions-MsFeatureData.R'
'do_adjustRtime-functions.R'
'functions-binning.R'
'do_detectFeatures-functions.R'
'do_findChromPeaks-functions.R'
'functions-Params.R'
'do_groupChromPeaks-functions.R'
'fastMatch.R'
'functions-Chromatogram.R'
'functions-utils.R'
'functions-IO.R'
'functions-MsFeatureData.R'
'functions-OnDiskMSnExp.R'
'functions-Params.R'
'functions-ProcessHistory.R'
'functions-XCMSnExp.R'
'functions-xcmsEIC.R'
Expand All @@ -70,6 +73,7 @@ Collate:
'functions-xcmsSet.R'
'init.R'
'matchpeaks.R'
'methods-Chromatogram.R'
'methods-IO.R'
'methods-MsFeatureData.R'
'methods-OnDiskMSnExp.R'
Expand Down
150 changes: 124 additions & 26 deletions NAMESPACE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,23 @@ importFrom("utils", "capture.output")
import("methods")
importFrom("ProtGenerics", "peaks")
importFrom("BiocGenerics", "updateObject", "fileName")
import("Biobase")
importFrom("graphics", "plot", "image", "boxplot")
## import("Biobase")
importFrom("Biobase", "AnnotatedDataFrame")
importClassesFrom("Biobase", "AnnotatedDataFrame", "Versioned")
importMethodsFrom("Biobase", "classVersion", "classVersion<-", "phenoData",
"phenoData<-", "pData", "rowMedians")

importFrom("graphics", "plot", "image", "boxplot", "matplot", "rect", "axis")
importFrom("mzR", "peaks", "close", "openMSfile", "header")
importFrom("lattice", "levelplot", "panel.rect", "panel.levelplot")
importFrom("plyr", "rbind.fill")
import("RColorBrewer")
import("BiocParallel")

## import("S4Vectors")
importClassesFrom("S4Vectors", "Rle", "DataFrame")
importFrom("S4Vectors", "split", "Rle", "DataFrame")
importMethodsFrom("S4Vectors", "as.matrix")

## Additional imports proposed by R CMD check:
importFrom("graphics", "abline", "barplot", "close.screen", "hist",
Expand Down Expand Up @@ -43,7 +50,8 @@ importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile"
"spectra", "impute", "isCentroided", "polarity", "[", "bin",
"clean", "featureNames", "filterAcquisitionNum", "filterMz",
"filterRt", "normalize", "pickPeaks", "removePeaks",
"removeReporters", "smooth", "trimMz")
"removeReporters", "smooth", "trimMz", "splitByFile", "[[",
"spectrapply", "peaksCount", "precursorMz")
importFrom("MSnbase", "as.data.frame.Spectrum")

export(
Expand Down Expand Up @@ -182,21 +190,34 @@ export(
"binYonX",
"breaks_on_binSize",
"breaks_on_nBins",
"do_detectFeatures_centWave",
"do_detectFeatures_massifquant",
"do_detectFeatures_matchedFilter",
"do_detectFeatures_MSW",
"do_detectFeatures_centWaveWithPredIsoROIs",
"do_detectFeatures_addPredIsoROIs",
"do_findChromPeaks_centWave",
"do_findChromPeaks_massifquant",
"do_findChromPeaks_matchedFilter",
"do_findPeaks_MSW",
"do_findChromPeaks_centWaveWithPredIsoROIs",
"do_findChromPeaks_addPredIsoROIs",
"imputeLinInterpol",
"useOriginalCode",
"setAs"
"setAs",
"do_groupChromPeaks_density",
"do_groupPeaks_mzClust",
"do_groupChromPeaks_nearest",
"Chromatogram",
"do_adjustRtime_peakGroups",
"processHistoryTypes",
"adjustRtimePeakGroups",
"plotAdjustedRtime",
"plotChromatogram",
"highlightChromPeaks",
"plotChromPeakDensity"
)

## New analysis methods
exportMethods(
"showError",
"detectFeatures"
"findChromPeaks",
"groupChromPeaks",
"adjustRtime"
)

## New Param classes
Expand All @@ -205,7 +226,14 @@ exportClasses(
"MatchedFilterParam",
"MassifquantParam",
"MSWParam",
"CentWavePredIsoParam"
"CentWavePredIsoParam",
"PeakDensityParam",
"MzClustParam",
"NearestPeaksParam",
"PeakGroupsParam",
"ObiwarpParam",
"GenericParam",
"FillChromPeaksParam"
)
## Param methods
exportMethods(
Expand Down Expand Up @@ -294,27 +322,86 @@ exportMethods(
"mzIntervalExtension<-",
"polarity",
"polarity<-",
"rtime",
"mz",
"intensity"
## PeakDensityParam
"sampleGroups",
"sampleGroups<-",
"bw",
"bw<-",
"minFraction",
"minFraction<-",
"minSamples",
"minSamples<-",
"maxFeatures",
"maxFeatures<-",
## MzClustParam
"absMz",
"absMz<-",
## NearestPeaksParam
"absRt",
"absRt<-",
"mzVsRtBalance",
"mzVsRtBalance<-",
"kNN",
"kNN<-",
"extraPeaks",
"extraPeaks<-",
"smooth",
"smooth<-",
"span",
"span<-",
"family",
"family<-",
## PeakGroupsParam
"peakGroupsMatrix",
"peakGroupsMatrix<-",
## ObiwarpParam
"centerSample",
"centerSample<-",
"response",
"response<-",
"distFun",
"distFun<-",
"gapInit",
"gapInit<-",
"gapExtend",
"gapExtend<-",
"factorDiag",
"factorDiag<-",
"factorGap",
"factorGap<-",
"localAlignment",
"localAlignment<-",
"initPenalty",
"initPenalty<-",
## FillChromPeaksParam
"expandMz",
"expandMz<-",
"expandRt",
"expandRt<-"
)
## Param class functions
export("CentWaveParam", "MatchedFilterParam", "MassifquantParam", "MSWParam",
"CentWavePredIsoParam")
"CentWavePredIsoParam", "PeakDensityParam", "MzClustParam",
"NearestPeaksParam", "PeakGroupsParam", "ObiwarpParam", "GenericParam",
"FillChromPeaksParam")
## Param class methods.

## New Classes
exportClasses("XCMSnExp", "MsFeatureData", "ProcessHistory", "XProcessHistory")
exportClasses("XCMSnExp", "MsFeatureData", "ProcessHistory",
"Chromatogram",
"XProcessHistory"
)
## New methods for these classes
exportMethods("hasDetectedFeatures",
"hasAlignedFeatures",
exportMethods("hasChromPeaks",
"hasFeatures",
"hasAdjustedRtime",
"adjustedRtime",
"adjustedRtime<-",
"featureGroups",
"featureGroups<-",
"features",
"features<-",
"featureDefinitions",
"featureDefinitions<-",
"featureValues",
"chromPeaks",
"chromPeaks<-",
"processHistory",
"fileIndex",
"processDate",
Expand All @@ -333,7 +420,18 @@ exportMethods("hasDetectedFeatures",
"removePeaks",
"smooth",
"dropAdjustedRtime",
"dropFeatureGroups",
"dropFeatures",
"spectra"
"dropFeatureDefinitions",
"dropChromPeaks",
"spectra",
"rtime",
"mz",
"intensity",
"aggregationFun",
"extractChromatograms",
"precursorMz",
"productMz",
"fillChromPeaks",
"as.data.frame",
"dropFilledChromPeaks",
"extractMsData"
)
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