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commit 1a3144aafc7f8a99575398d5c7d8d3ff0ae6870f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jul 21 06:55:18 2017 +0200

    Documentation tidying.

commit f7825ada4f743ff83ea71669b888d7b1c42d47fd
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jul 21 06:39:29 2017 +0200

    Re-enable sleep parameter in findPeaks.matchedFilter

    - Add sleep parameter to do_findChromPeaks_matchedFilter.
    - Re-enable sleep parameter in findChromPeaks.matchedFilter.
    - Update relevant documentation.

commit 5beacd4db53f7caa65ad6b4dea135ebf5be37c83
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jul 18 06:58:01 2017 +0200

    Re-enable the sleep parameter in centWave

    - Re-add plotting functionality to the do_findChromPeaks_centWave function. Add
      the parameter sleep.

commit 46079088821e45f4ed9e8d933de5af40af259c94
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jul 14 09:30:23 2017 +0200

    Fix unit test to work with recent change in MSnbase

commit 9c18189766d59ab91a51f8e840a54b2832ea1259
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 12 16:06:14 2017 +0200

    Some example performance tuning

commit 741073f6f56aa8ee29ca370b751827b5844ebe1a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 12 15:05:19 2017 +0200

    Fix bracket errors

commit 80a47b4d43e5eedadd98446f0392d6a6b6b36dc4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 12 15:01:21 2017 +0200

    Fix parallel processing for Windows systems

    - Fix parallel processing in unit tests and vignettes to use SnowParam on
      non-unix systems.

commit 7ff49c94929461100da1b24b5bc40073d381d1cc
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 12 10:36:42 2017 +0200

    Small fixes to the adjustDriftWithModel function

commit 02ebe57154eadf18d22745d5f7ab49fb849d5b34
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 12 07:56:51 2017 +0200

    Add plotChromPeakImage function (issue #154)

    - Add the plotChromPeakImage function.
    - Add related unit tests, documentation and update vignette.
    - Add a source file with some first (unexported) data normalization functions.

commit 9609d4dda044bf8cd10aa80632fabb0096131576
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jul 11 13:03:42 2017 +0200

    Add plotChromPeaks function (issue #154)

commit 7aa5ef0add5391e10b237f33bc36fde934b595f0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 10 11:07:54 2017 +0200

    Read polarity information from mzXML files

    - Read also polarity information from mzXML files (issue #192).
    - Don't import aggregationFun and productMz from MSnbase.

commit 8d829a2da4b88a5113269ffb579e4d13aa6cb8f4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 10 10:42:25 2017 +0200

    Import aggregationFun and productMz as functions

    - aggregationFun and productMz were changed from methods to functions in MSnbase
      - import these functions.

commit 587b2d14e55ec553c3d2c01b35c3992d0599436e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jun 21 15:07:48 2017 +0200

    Import all Chromatogram functionality from MSnbase

    - Import all required functions and classes related to chromatogram data from
      MSnbase.
    - Update all examples, unit tests and vignettes to use the new methods.
    - Deprecated extractChromatograms and plotChromatogram.
    - Fix an issue that caused an uninformative error message when peak detection
      was performed on an MS2 only OnDiskMSnExp (issue #190).
    - Add argument msLevel to the findChromPeaks methods allowing to perform
      chromatographic peak detection on MS > 1 (enabling SWATH issue #190).

commit b138398ba618c07368638f1be80c675dfec15cba
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jun 20 12:33:43 2017 +0200

    Import Chromatogram class and methods

    - Import Chromatogram object.
    - Deprecate extractChromatograms.
    - import chromatogram,OnDiskMSnExp.

commit 1eba1d17b462791f890e1d04282fbd0257259ecd
Merge: 1b1e42a 710a8f9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jun 16 13:18:19 2017 +0200

    Merge branch 'devel' into xcms3

commit 1b1e42a1d39efeabba6e9acf52bf9b74c33d6937
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jun 16 13:16:42 2017 +0200

    Remove Chromatogram class

commit 710a8f9d44f3e330fe0072bf02cc9ac8548bf120
Merge: 7ef7059 056dd82
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Fri Jun 16 07:25:02 2017 +0200

    Merge branch 'biocdevel' into devel

commit bcac6ab7afad578085d3a83a8a911812c35cf79a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jun 15 10:19:01 2017 +0200

    Tune unit tests and vignettes #187

commit 7ef70598754cffc9e896ddb3358f62471e0d16cb
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jun 13 16:32:36 2017 +0200

    Fix issue #188

    - For files with unknown file extension determine the file type from its
      content.
    - Add related unit tests.

commit a245c74557fa2937b94637dd9ec36183bc62491d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jun 12 16:17:11 2017 +0200

    Tune some unit tests and examples

    - Related to issue #187: tune some unit tests and examples.

commit 8e8db555541e71d929e06e8afb5e2738f0201147
Merge: 3d03ef5 82fe82b
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Jun 6 12:42:12 2017 +0200

    Merge branch 'biocdevel' into devel

commit 3d03ef5433aca18593e4fc4ee126ca41dbf753a3
Merge: bafb6de 8c1220e
Author: Johannes Rainer <jotsetung@users.noreply.github.com>
Date:   Tue Jun 6 10:54:35 2017 +0200

    Merge pull request #185 from sneumann/issue184

    Fix issue #184

commit 8c1220eaf7f866572e726b11baaa7672c514c237
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jun 5 17:26:53 2017 +0200

    Fix issue #184

    - Add parameter sleep to the do_groupChromPeaks_density function to ensure
      backward compatibility with the old group.density code.

commit bafb6de6bb3939a45b108865eac69ddaef7c4a51
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 31 13:04:34 2017 +0200

    Fix some more typos and tidy roxygen text

commit 5249622a585b8bea916c14a0683a158dd7210a2f
Merge: ffc9e39 54cc415
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 31 12:45:50 2017 +0200

    Merge branch 'devel' into xcms3

commit ffc9e39dd8570fa51e9c4abd1b99864bdd25b7fd
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 31 12:42:36 2017 +0200

    Fix for issue #181

    - issue #181: isCentroided returns NA is there are too peaks in a spectrum. The
      methods in xcms (findChromPeaks,OnDiskMSnExp,CentWaveParam) check first
      whether the first spectrum is centroided, if an NA is returned isCentroided
      is called on all spectra and based on that the function determines whether the
      data set is centroided.

commit 54cc4154926ec6123b237ce3a0433c1fef13e5e7
Merge: aabdf5c f9bbe42
Author: Johannes Rainer <jotsetung@users.noreply.github.com>
Date:   Wed May 31 10:53:52 2017 +0200

    Merge pull request #183 from stanstrup/patch-6

    typos

commit f9bbe4287ca6f1560e33fccaad63842b58d57dfd
Author: Jan Stanstrup <stanstrup@gmail.com>
Date:   Wed May 31 10:51:34 2017 +0200

    typos

commit aabdf5c29daddd60aae2c7b12512dcf1f6d5bc1c
Merge: 4dfbc01 13f69c8
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Sun May 28 18:56:31 2017 +0200

    Merge branch 'biocdevel' into devel

commit 4dfbc01c1ec656fed8e0d3a4e262193f1061ebb3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 26 11:52:55 2017 +0200

    Fix issue #180

commit 8dfccd382b73c3f772b4a80b7d2fbe38b57c0a96
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 26 08:56:17 2017 +0200

    Update NEWS.

commit d290cbeb8d57a69305f7f7315135fa26f6eb80b5
Merge: 56c43dd d2d4b7a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu May 25 17:17:59 2017 +0200

    Merge branch 'devel' into xcms3

commit d2d4b7a2a18a9a1620eaa52e94dc81edb2c939e9
Merge: f11aac4 d9baa6c
Author: Johannes Rainer <jotsetung@users.noreply.github.com>
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 <stanstrup@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Thu May 18 15:36:54 2017 +0200

    Fix for issue #175

    - Disable original xcms-preprocessing vignette.

commit 36535df5d03137a1d3db62fbf7a9f85c7fdaf8a9
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri May 5 13:21:14 2017 +0200

    Fix for bug introduced into plotChromPeakDensity

commit ad6aa2bf4bec129147c1407d0325f531dcf1fcb0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 5 13:03:00 2017 +0200

    Add Jan Stanstrup's fix also to the plotChromPeakDensity function

commit 906be43e92aee5ac54b97ee795ada7848cbae5c5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 5 13:00:30 2017 +0200

    Update news.

commit 11ed73c97b5c1ea28354172da7f639eff85bae38
Merge: e90b74e f11aac4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 5 12:59:04 2017 +0200

    Merge branch 'devel' into xcms3

commit f11aac4020319d991b845154e492f1031f946888
Author: jotsetung <johannes.rainer@gmail.com>
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 <jotsetung@users.noreply.github.com>
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 <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Fri May 5 09:49:28 2017 +0200

    Merge branch 'biocdevel' into devel

commit 58e35e588c0f4654f013f06933356b0d232f1f99
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 77b0396c54e2afe61de1df09271ec1ce427781e3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 21 15:25:27 2017 +0200

    Fix bug in plotChromatogram

commit 612cecfc868a55b94c43cf01d16b15ea6c56418c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 21 14:27:48 2017 +0200

    Ensure plotChromatogram doesn't break if no data available

commit af6eea822cb9edb1d9d979289617b022b6947584
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Fri Apr 14 19:20:26 2017 +0200

    Merge branch 'biocdevel' into devel

commit f775cbb7336e160ff7157d5e897c5cd1a0e93d8c
Merge: aa9f1d3 30bb9b2
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Apr 13 18:59:42 2017 +0200

    Merge branch 'xcms3' into devel

commit 30bb9b270ff90a4a54b8e752f3abf8dd609ee811
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Apr 13 18:57:46 2017 +0200

    Update date

commit 9d507248152612eabc049cd887f838aa525545d9
Author: jotsetung <johannes.rainer@gmail.com>
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 60ff5957cf9ef6a7729710eb2fdb823209fa8d62
Author: Jan Stanstrup <stanstrup@gmail.com>
Date:   Tue Apr 11 11:01:47 2017 +0200

    additional fixes for #160

commit 959004a09888b236111bc0ef5a9f829a5558c174
Author: Jan Stanstrup <stanstrup@gmail.com>
Date:   Tue Apr 11 10:57:25 2017 +0200

    devel patch for # 160

commit 0b26f47f3bb48080c5691af82631e176e6312018
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Fri Mar 31 13:58:31 2017 +0200

    Merge branch 'biocdevel' into devel

commit 828883b412f7973f10eacbd58eac2744500ecb13
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Mar 31 07:50:44 2017 +0200

    Updates to the vignette

commit cbe41fac512d7ed267b3d1a36bccb023fe776615
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Mar 17 08:06:52 2017 +0100

    Change order of alignment and correspondence in XCMSnExp,show

commit f8148d567b9e2f406755f27149334a103f0b23b4
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Tue Mar 14 15:53:49 2017 +0100

    Merge branch 'devel' into xcms3

commit b4c48850e6976bc599fc02bb5d224bd69ae370b6
Author: jotsetung <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Fri Mar 10 23:09:00 2017 +0100

    Merge branch 'biocdevel' into devel

commit e8dbb4c094b0cbaa6a962320047f941f52474207
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Mar 10 11:12:53 2017 +0100

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

commit cf6b1bca8d966a9bc2ffc34d68bfedb76c4eeb93
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Mar 9 17:04:16 2017 +0100

    Remove debug centWave version debug message

commit e9f39ecd6540aae7ba4a438d9ca8b26a1e8e80ff
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 8 08:44:30 2017 +0100

    Extend new_functionality vignette.

commit 572f2ebe0d840929dc4db7fb671f9a54016f7861
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Mon Mar 6 14:35:01 2017 +0100

    Remove commented old matchedFilter test functions.

commit e899b923086b8c540f26a0b1fdb468eb0cd701a3
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Mar 3 13:58:52 2017 +0100

    Extend show method for XCMSnExp

commit c9c061fd76e883d33431830a4277d721678af060
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Mar 3 13:36:52 2017 +0100

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

commit e51387f7cc7ec952ad258b4b9bd6d46897e582e3
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Mar 3 10:41:43 2017 +0100

    Add @filled slot for XCMSnExp to xcmsSet conversion

commit 083fd4b2594ae8e5703ca04ca527ff6a12453fa4
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Thu Mar 2 13:12:28 2017 +0100

    o Remove debug messages from xcmsSet.

commit d469000b45403204e8796dd1de0dd07fabf7e32c
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Mon Feb 27 22:11:31 2017 +0100

    Merge branch 'devel' into xcms3

commit 8e44a7bb32b532da9fc86c07a7676c1223a6acd5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 27 18:47:34 2017 +0100

    Update NEWS

commit 2d670e210408e778cd896553632e0e9b3969b0ac
Author: jotsetung <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Fri Feb 24 22:12:22 2017 +0100

    Merge branch 'biocdevel' into devel

commit 78a98b1e8c2612a847382ff741da49a90786c6c0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Feb 24 08:38:39 2017 +0100

    Add columne "is_filled" to chromPeaks matrix

commit 1743262d1d03865461bc489bf76fc0a566608f4e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 23 18:58:44 2017 +0100

    Add findChromPeaks for XCMSnExp objects (issue #128)

commit 8068dbeb2d955121179c6974b94c6aa7d7b0d610
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Wed Feb 22 11:06:19 2017 +0100

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

commit 2ae5eafdebe4c225d3a1de7b194a89093507d109
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Wed Feb 15 09:39:04 2017 +0000

    Ensure memory cleanup in parallel findPeaks for xcmsSet

commit 6da82fc146eb80e3058ce56cfe2bc536818fce82
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Feb 8 12:15:02 2017 +0100

    Minor changes to Chromatogram

    o Don't export Chromatogram.

commit c4bca930c1f897e1fe3b3db6c01cfb6f7c456d27
Author: jotsetung <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Fri Feb 3 09:59:01 2017 +0100

    Merge branch 'biocdevel' into devel

commit b0deb92a9b8df81fe7b2ea6e2129ae46bc282cfa
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Feb 3 09:20:54 2017 +0100

    Bump version and update NEWS.

commit 70040008b630ede4a8c5ff569fce27bf798a4616
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Thu Feb 2 18:48:02 2017 +0100

    Bump version.

commit 0c9b416ea9128ecbbce3ce567a71d7462b776cdb
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 2 18:45:06 2017 +0100

    Small internal changes.

commit 09eb5e3f5e784157e8b50e159cef9c05cf725bc8
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 2 15:21:15 2017 +0100

    Small code cleanup.

commit 00fd415e0b14070b3bf9a417283b98a9a888c065
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 2 15:01:58 2017 +0100

    Update NEWS.

commit 806d79351a46d5369d2e056010ca33f6d7c5d5f4
Merge: 2d2ecf8 6e0381e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 2 14:48:35 2017 +0100

    Merge branch 'devel' into xcms3

commit 2d2ecf85d66ce24309499c60834448694ac5eb60
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 2 14:18:48 2017 +0100

    Fix unit test error on R-3.2.3

commit 7720ea5c0de35552ca8c25e782e1e9df7ab47023
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Tue Jan 24 12:18:08 2017 +0100

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

commit 5d602d2185665c9feac159dacda58fdbaa36bfed
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Jan 20 16:26:56 2017 +0100

    Remove commented code.

commit 9b88134182343a19992fe99100d39c0c62b9242b
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Jan 20 13:15:36 2017 +0100

    Fix warnings in group.nearest (issue #109)

commit ec0daf60ed1c6d01e696dc7e927c25d10b651912
Merge: 8fd3010 8312b64
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jan 20 11:10:29 2017 +0100

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

commit 8fd301034eefa35e87dbbccb47aec86643e79297
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Tue Jan 17 10:19:10 2017 +0100

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

commit 9edb01c2d9986d15d48d65ce95ed00edc86901bc
Author: jotsetung <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
Date:   Tue Jan 17 08:28:38 2017 +0100

    Bump version and adapt NEWS

commit 87a57f1c4d1ab4da77093dc529ed4def9b1bc0e2
Merge: 5e288f4 62452c2
Author: Steffen Neumann <sneumann@ipb-halle.de>
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 <sneumann@ipb-halle.de>
Date:   Mon Jan 16 22:57:07 2017 +0100

    Merge branch 'biocdevel' into devel

commit 62452c2b5204f515e57579aaa8c614173c44750b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jan 16 12:57:22 2017 +0100

    Removed , in DESCRIPTION

commit bdc3d65b646447f4b7fef7ba650623d2bcacb87f
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Jan 13 13:33:54 2017 +0100

    Fix issue #102

commit 95f5c30fdd727e0419de928553121d204e032ae4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jan 13 13:29:26 2017 +0100

    Fix issue #91.

    o Replay the changes made by Jan Stanstrup.

commit 839fdb369875f895c06d627dedbe5161e3600f2c
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Thu Jan 12 16:21:50 2017 +0100

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

commit 223798c30f8852d3c4696f4284facbe4152a08c8
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jan 12 07:58:19 2017 +0100

    Update NEWS.

commit 277324fec07683db2b08e09c0077ce243f9d327f
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Mon Jan 9 16:01:17 2017 +0100

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

commit 48055c072e5589fa2fd3351b5a14de0b5bbc3a9b
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Mon Jan 2 21:22:48 2017 +0100

    Fix failed execution of unit tests

commit a1122065a96cf6e69088417d82fe987cda188cd5
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Sun Dec 25 18:49:49 2016 +0100

    Merge branch 'devel' into xcms3

commit e92a02d2b0bb24bb9c58b615879f430fa35a9b61
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Thu Dec 22 16:22:15 2016 +0100

    Extend show method for XCMSnExp objects.

commit a58cf39f9ebde3e6dc3ee94795fd3cb9addb18e5
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
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 <sneumann@ipb-halle.de>
Date:   Tue Dec 20 21:43:15 2016 +0100

    Merge branch 'stanstrup-patch-3' into devel

commit fef11aac12ca51f227ac9302fe960997563e11a3
Merge: 5160700 ba80552
Author: Steffen Neumann <sneumann@ipb-halle.de>
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 <sneumann@ipb-halle.de>
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 <sneumann@ipb-halle.de>

    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 <sneumann@ipb-halle.de>

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

commit 647e2f9c5fc7e6ea40d839c9846b07d668a95f0d
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Dec 20 21:34:30 2016 +0100

    adapted manpage for plotQC

commit cf29b17d73c32bb0b89f7b7166fcb9cf9decec1e
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Dec 20 21:32:50 2016 +0100

    merged xcms3 branch, added return value to plotQC()

commit ba805525dda98a90d9dd4682fbbdd0318bbab01d
Author: Jan Stanstrup <stanstrup@gmail.com>
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 <johannes.rainer@gmail.com>
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 <sneumann@ipb-halle.de>
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 <johannes.rainer@gmail.com>
Date:   Tue Dec 13 08:16:05 2016 +0100

    Add CentWavePredIsoParam class

    o Add CentWavePredIsoParam class, documentation and unit tests.

commit 515b8141ab02e3726cdc52cdb69f130a5ef9f689
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Sun Dec 11 19:21:14 2016 +0100

    Merge branch 'devel' into xcms3

commit 02444fdc4f3e2264d7ff85e7320e9df955969379
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Sat Dec 10 22:19:13 2016 +0100

    Start implementing the do function for withAddIsotopes

commit cba193bdeac458b978628c66d02a9dfdef69e1c6
Author: Jan Stanstrup <stanstrup@gmail.com>
Date:   Fri Dec 9 11:05:45 2016 +0100

    More informative warning.

commit 9dc277bfeebd257b967645e61fb817c732ce16a3
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <jotsetung@users.noreply.github.com>
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 <htreutle@ipb-halle.de>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Sun Nov 27 18:44:50 2016 +0100

    Just some comments

commit dd8cbd3c8f5aaa6e8633f7aee5185f4df009d9d4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Nov 27 08:34:34 2016 +0100

    Add MassifquantParam class

    o Add a MassifquantParam class (issue #84).

commit a6bfa83e3d5cce6dbfc4ce9416aaff873275d4ca
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Nov 25 11:52:56 2016 +0100

    Add warning if data is not in centroid mode for centWave

commit 284408213e7c410e2a09e68697c737524851ed03
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
Date:   Fri Oct 21 09:26:36 2016 +0200

    Update the new_functionality.Rmd vignette.

commit 31139f05c72360f84ed7aec20b7a19efadf81928
Merge: fa2fb9b fa4a97f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Oct 21 09:20:17 2016 +0200

    Merge branch 'devel' into xcms3

commit fa2fb9b054e06bfa4fb25ca8ac1eeb1286b77137
Author: jotsetung <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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).

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sneumann committed Jul 21, 2017
1 parent e85e690 commit d2b7b8c
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9 changes: 4 additions & 5 deletions DESCRIPTION
View file
@@ -1,6 +1,6 @@
Package: xcms
Version: 2.99.3
Date: 2017-06-13
Version: 2.99.5
Date: 2017-07-14
Title: LC/MS and GC/MS Data Analysis
Author: Colin A. Smith <csmith@scripps.edu>,
Ralf Tautenhahn <rtautenh@gmail.com>,
Expand All @@ -14,7 +14,7 @@ Depends:
methods,
Biobase,
BiocParallel (>= 1.8.0),
MSnbase (>= 2.1.10)
MSnbase (>= 2.3.8)
Imports:
mzR (>= 1.1.6),
BiocGenerics,
Expand Down Expand Up @@ -61,19 +61,18 @@ Collate:
'functions-Params.R'
'do_groupChromPeaks-functions.R'
'fastMatch.R'
'functions-Chromatogram.R'
'functions-utils.R'
'functions-IO.R'
'functions-OnDiskMSnExp.R'
'functions-ProcessHistory.R'
'functions-XCMSnExp.R'
'functions-normalization.R'
'functions-xcmsEIC.R'
'functions-xcmsFragments.R'
'functions-xcmsRaw.R'
'functions-xcmsSet.R'
'init.R'
'matchpeaks.R'
'methods-Chromatogram.R'
'methods-IO.R'
'methods-MsFeatureData.R'
'methods-OnDiskMSnExp.R'
Expand Down
23 changes: 11 additions & 12 deletions NAMESPACE
View file
Expand Up @@ -2,7 +2,7 @@ useDynLib(xcms)

importFrom("utils", "capture.output")
import("methods")
importFrom("ProtGenerics", "peaks")
importFrom("ProtGenerics", "peaks", "chromatogram")
importFrom("BiocGenerics", "updateObject", "fileName")
## import("Biobase")
importFrom("Biobase", "AnnotatedDataFrame")
Expand Down Expand Up @@ -44,15 +44,17 @@ importFrom("RANN", "nn2")
importFrom("MassSpecWavelet", "peakDetectionCWT", "tuneInPeakInfo")

## MSnbase:
importClassesFrom("MSnbase", "MSnExp", "pSet", "OnDiskMSnExp")
importClassesFrom("MSnbase", "MSnExp", "pSet", "OnDiskMSnExp", "Chromatogram",
"Chromatograms")
importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile",
"filterFile", "filterMsLevel", "msLevel", "scanIndex",
"spectra", "impute", "isCentroided", "polarity", "[", "bin",
"clean", "featureNames", "filterAcquisitionNum", "filterMz",
"filterRt", "normalize", "pickPeaks", "removePeaks",
"removeReporters", "smooth", "trimMz", "splitByFile", "[[",
"spectrapply", "peaksCount", "precursorMz")
importFrom("MSnbase", "as.data.frame.Spectrum")
"spectrapply", "peaksCount", "precursorMz", "chromatogram",
"plot", "fData", "fData<-")
importFrom("MSnbase", "as.data.frame.Spectrum", "Chromatogram", "Chromatograms")

export(
"etg",
Expand Down Expand Up @@ -202,14 +204,15 @@ export(
"do_groupChromPeaks_density",
"do_groupPeaks_mzClust",
"do_groupChromPeaks_nearest",
"Chromatogram",
"do_adjustRtime_peakGroups",
"processHistoryTypes",
"adjustRtimePeakGroups",
"plotAdjustedRtime",
"plotChromatogram",
"highlightChromPeaks",
"plotChromPeakDensity"
"plotChromPeakDensity",
"plotChromPeaks",
"plotChromPeakImage"
)

## New analysis methods
Expand Down Expand Up @@ -388,7 +391,6 @@ export("CentWaveParam", "MatchedFilterParam", "MassifquantParam", "MSWParam",

## New Classes
exportClasses("XCMSnExp", "MsFeatureData", "ProcessHistory",
"Chromatogram",
"XProcessHistory"
)
## New methods for these classes
Expand Down Expand Up @@ -426,12 +428,9 @@ exportMethods("hasChromPeaks",
"rtime",
"mz",
"intensity",
"aggregationFun",
"extractChromatograms",
"precursorMz",
"productMz",
"fillChromPeaks",
"as.data.frame",
"dropFilledChromPeaks",
"extractMsData"
"extractMsData",
"chromatogram"
)
3 changes: 0 additions & 3 deletions R/AllGenerics.R
View file
Expand Up @@ -16,8 +16,6 @@ setGeneric("adjustRtime", function(object, param, ...)
setGeneric("adjustedRtime", function(object, ...) standardGeneric("adjustedRtime"))
setGeneric("adjustedRtime<-", function(object, value)
standardGeneric("adjustedRtime<-"))
setGeneric("aggregationFun", function(object, ...)
standardGeneric("aggregationFun"))
setGeneric("ampTh", function(object, ...) standardGeneric("ampTh"))
setGeneric("ampTh<-", function(object, value) standardGeneric("ampTh<-"))
setGeneric("AutoLockMass", function(object) standardGeneric("AutoLockMass"))
Expand Down Expand Up @@ -283,7 +281,6 @@ setGeneric("processParam<-", function(object, value)
setGeneric("processType", function(object, ...) standardGeneric("processType"))
setGeneric("processType<-", function(object, value) standardGeneric("processType<-"))
setGeneric("processHistory", function(object, ...) standardGeneric("processHistory"))
setGeneric("productMz", function(object, value) standardGeneric("productMz"))
setGeneric("profinfo", function(object) standardGeneric("profinfo"))
setGeneric("profinfo<-", function(object, value) standardGeneric("profinfo<-"))
setGeneric("profMat", function(object, ...) standardGeneric("profMat"))
Expand Down
90 changes: 21 additions & 69 deletions R/DataClasses.R
View file
Expand Up @@ -387,6 +387,12 @@ setClass("XProcessHistory",
#' @seealso \code{\link{findPeaks}} for the \emph{old} peak detection
#' methods.
#'
#' \code{\link{plotChromPeaks}} to plot identified chromatographic peaks
#' for one file.
#'
#' \code{\link{highlightChromPeaks}} to highlight identified chromatographic
#' peaks in an extracted ion chromatogram plot.
#'
#' @author Johannes Rainer
NULL
#> NULL
Expand Down Expand Up @@ -725,8 +731,9 @@ NULL
#'
#' @examples
#'
#' ## Create a MatchedFilterParam object
#' mfp <- MatchedFilterParam(binSize = 0.5)
#' ## Create a MatchedFilterParam object. Note that we use a unnecessarily large
#' ## binSize parameter to reduce the run-time of the example.
#' mfp <- MatchedFilterParam(binSize = 5)
#' ## Change snthresh parameter
#' snthresh(mfp) <- 15
#' mfp
Expand All @@ -738,7 +745,7 @@ NULL
#' library(MSnbase)
#' fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
#' full.names = TRUE)
#' raw_data <- readMSData2(fls)
#' raw_data <- readMSData2(fls[1:2])
#' ## Perform the chromatographic peak detection using the settings defined
#' ## above. Note that we are also disabling parallel processing in this
#' ## example by registering a "SerialParam"
Expand Down Expand Up @@ -1657,7 +1664,7 @@ NULL
#' p
#'
#' ##############################
#' ## Chromatographi peak detection and grouping.
#' ## Chromatographic peak detection and grouping.
#' ##
#' ## Below we perform first a chromatographic peak detection (using the
#' ## matchedFilter method) on some of the test files from the faahKO package
Expand Down Expand Up @@ -2255,8 +2262,8 @@ setClass("MsFeatureData", contains = c("environment", "Versioned"),
#' the feature definitions representing the peak grouping results.
#' \code{\link{adjustRtime}} for retention time adjustment methods.
#'
#' \code{\link{extractChromatograms}} to extract MS data as
#' \code{\link{Chromatogram}} objects.
#' \code{\link[MSnbase]{chromatogram}} to extract MS data as
#' \code{\link[MSnbase]{Chromatogram}} objects.
#'
#' \code{\link{extractMsData}} for the method to extract MS data as
#' \code{data.frame}s.
Expand All @@ -2272,7 +2279,7 @@ setClass("MsFeatureData", contains = c("environment", "Versioned"),
#' ## Now we perform a chromatographic peak detection on this data set using the
#' ## matched filter method. We are tuning the settings such that it performs
#' ## faster.
#' mfp <- MatchedFilterParam(binSize = 4)
#' mfp <- MatchedFilterParam(binSize = 6)
#' xod <- findChromPeaks(od, param = mfp)
#'
#' ## The results from the peak detection are now stored in the XCMSnExp
Expand Down Expand Up @@ -2302,12 +2309,15 @@ setClass("MsFeatureData", contains = c("environment", "Versioned"),
#' ## spectra method which returns Spectrum objects containing all raw data.
#' ## Note that all these methods read the information from the original input
#' ## files and subsequently apply eventual data processing steps to them.
#' head(mz(xod, bySample = TRUE))
#' mzs <- mz(xod, bySample = TRUE)
#' length(mzs)
#' lengths(mzs)
#'
#' ## Reading all data
#' spctr <- spectra(xod)
#' ## The full data could also be read using the spectra data, which returns
#' ## a list of Spectrum object containing the mz, intensity and rt values.
#' ## spctr <- spectra(xod)
#' ## To get all spectra of the first file we can split them by file
#' head(split(spctr, fromFile(xod))[[1]])
#' ## head(split(spctr, fromFile(xod))[[1]])
#'
#' ############
#' ## Filtering
Expand Down Expand Up @@ -2395,61 +2405,3 @@ setClass("XCMSnExp",
}
)

#' @title Representation of chromatographic MS data
#'
#' @description The \code{Chromatogram} class is designed to store
#' chromatographic MS data, i.e. pairs of retention time and intensity
#' values. Instances of the class can be created with the
#' \code{Chromatogram} constructor function but in most cases the dedicated
#' methods for \code{\link{OnDiskMSnExp}} and \code{\link{XCMSnExp}}
#' objects extracting chromatograms should be used instead (i.e. the
#' \code{\link{extractChromatograms}}).
#'
#' @details The \code{mz}, \code{filterMz}, \code{precursorMz} and
#' \code{productMz} are stored as a \code{numeric(2)} representing a range
#' even if the chromatogram was generated for only a single ion (i.e. a
#' single mz value). Using ranges for \code{mz} values allow this class to
#' be used also for e.g. total ion chromatograms or base peak chromatograms.
#'
#' The slots \code{precursorMz} and \code{productMz} allow to represent SRM
#' (single reaction monitoring) and MRM (multiple SRM) chromatograms. As
#' example, a \code{Chromatogram} for a SRM transition 273 -> 153 will have
#' a \code{@precursorMz = c(273, 273)} and a
#' \code{@productMz = c(153, 153)}.
#'
#' @rdname Chromatogram-class
#'
#' @export
#'
#' @author Johannes Rainer
#'
#' @seealso \code{\link{extractChromatograms}} for the method to extract
#' \code{Chromatogram} objects from \code{\link{XCMSnExp}} or
#' \code{\link[MSnbase]{OnDiskMSnExp}} objects.
#'
#' \code{\link{plotChromatogram}} to plot \code{Chromatogram} objects.
setClass("Chromatogram",
slots = c(
rtime = "numeric",
intensity = "numeric",
mz = "numeric",
filterMz = "numeric",
precursorMz = "numeric", ## Or call that Q1mz?
productMz = "numeric", ## Or call that Q3mz?
fromFile = "integer",
aggregationFun = "character"
),
contains = "Versioned",
prototype = prototype(
rtime = numeric(),
intensity = numeric(),
mz = c(NA_real_, NA_real_),
filterMz = c(NA_real_, NA_real_),
precursorMz = c(NA_real_, NA_real_),
productMz = c(NA_real_, NA_real_),
fromFile = integer(),
aggregationFun = character()
),
validity = function(object)
validChromatogram(object)
)
103 changes: 103 additions & 0 deletions R/Deprecated.R
View file
Expand Up @@ -332,3 +332,106 @@ xcmsClusterApply <- function(cl, x, fun, msgfun=NULL, ...) {
}

}

setMethod("extractChromatograms",
signature(object = "OnDiskMSnExp"),
function(object, rt, mz, aggregationFun = "sum", missing = NA_real_) {
.Deprecated(msg = paste0("Use of 'extractChromatograms' is ",
"deprecated, please use 'chromatogram' ",
"instead."))
chromatogram(object, rt = rt, mz = mz,
aggregationFun = aggregationFun, missing = missing)
})

plotChromatogram <- function(x, rt, col = "#00000060",
lty = 1, type = "l", xlab = "retention time",
ylab = "intensity", main = NULL, ...) {
.Deprecated(msg = paste0("Use of 'plotChromatogram' is deprecated, please ",
"use 'plot' instead."))
if (!is.list(x) & !is(x, "Chromatogram"))
stop("'x' should be a Chromatogram object or a list of Chromatogram",
" objects.")
if (is(x, "Chromatogram"))
x <- list(x)
isOK <- lapply(x, function(z) {
if (is(z, "Chromatogram")) {
return(TRUE)
} else {
if (is.na(z))
return(TRUE)
}
FALSE
})
if (any(!unlist(isOK)))
stop("if 'x' is a list it should only contain Chromatogram objects")
## Subset the Chromatogram objects if rt provided.
if (!missing(rt)) {
rt <- range(rt)
x <- lapply(x, function(z) {
if (is(z, "Chromatogram"))
filterRt(z, rt = rt)
})
}
if (length(col) != length(x)) {
col <- rep(col[1], length(x))
}
## If main is NULL use the mz range.
if (is.null(main)) {
mzr <- range(lapply(x, mz), na.rm = TRUE, finite = TRUE)
main <- paste0(format(mzr, digits = 7), collapse = " - ")
}
## Number of measurements we've got per chromatogram. This can be different
## between samples, from none (if not a single measurement in the rt/mz)
## to the number of data points that were actually measured.
lens <- unique(lengths(x))
max_len <- max(lens)
max_len_vec <- rep_len(NA, max_len)
## Generate the matrix of rt values, columns are samples, rows retention
## time values. Fill each column with NAs up to the maximum number of values
## we've got in a sample/file.
rts <- do.call(cbind, lapply(x, function(z) {
cur_len <- length(z)
if (cur_len == 0)
max_len_vec
else {
## max_len_vec[,] <- NA ## don't need that. get's copied.
max_len_vec[seq_len(cur_len)] <- rtime(z)
max_len_vec
}
}))
## Same for the intensities.
ints <- do.call(cbind, lapply(x, function(z) {
cur_len <- length(z)
if (length(z) == 0)
max_len_vec
else {
## max_len_vec[,] <- NA ## don't need that. get's copied.
max_len_vec[seq_len(cur_len)] <- intensity(z)
max_len_vec
}
}))
## Define the x and y limits
x_lim <- c(0, 1)
y_lim <- c(0, 1)
if (all(is.na(rts)))
if (!missing(rt))
x_lim <- range(rt)
else
x_lim <- range(rts, na.rm = TRUE, finite = TRUE)
if (!all(is.na(ints)))
y_lim <- range(ints, na.rm = TRUE, finite = TRUE)
## Identify columns that have only NAs in either intensity or rt - these
## will not be plotted.
keepCol <- which(apply(ints, MARGIN = 2, function(z) any(!is.na(z))) |
apply(rts, MARGIN = 2, function(z) any(!is.na(z))))
## Finally plot the data.
if (length(keepCol)) {
matplot(x = rts[, keepCol, drop = FALSE],
y = ints[, keepCol, drop = FALSE], type = type, lty = lty,
col = col[keepCol], xlab = xlab, ylab = ylab, main = main,
...)
} else
plot(x = 3, y = 3, pch = NA, xlab = xlab, ylab = ylab, main = main,
xlim = x_lim, ylim = y_lim)
}

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