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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).

commit 9611dae1e9689d67cbbfba2ceb1b5d215b921adc
Author: jotsetung <johannes.rainer@gmail.com>
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: hpages@fhcrc.org <hpages@fhcrc.org@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: hpages@fhcrc.org <hpages@fhcrc.org@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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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 <johannes.rainer@gmail.com>
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-devel' into devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@121386 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 05749105ac97b83938dc11705a57a8c1165522c6
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Sep 26 14:26:19 2016 +0000

    updated NEWS and bumped version

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@121385 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 39e1823fb1ed38a76c77b8e061af0024a7d09c7f
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Mon Sep 26 15:22:00 2016 +0200

    fixed WARNINGS

commit f82432a125e222d9a9ab475cdd47d36c2da1b458
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Sep 26 08:19:46 2016 +0200

    Add [ method for xcmsRaw objects

    o Implement a [ method for xcmsRaw objects allowing to sub-set the
      object to specified scans/spectra.
    o Implement the do_detectFeatures_massifquant function.
    o Unit tests for the above method/function.

commit 9f35b91e6c6381ce6892d15b95b5ab9b70c02c3f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 23 13:48:10 2016 +0200

    Fix NEWS and remove unused variables from C code

    o Remove unused variables from C/C++ code.

commit 536aa23e1c07bedae1083ff7bee400efdc8dcc79
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 23 13:16:24 2016 +0200

    Fix issue #59

    o Fix passing arguments in the wrong order in do_detectFeatures_MSW.
    o Fix a small bug in diffreport (wrong variable name for a directory).

commit 873b11d4f8d15c09e294ef3983ad62f8ac43a5ee
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 23 12:35:38 2016 +0200

    Fix issue #58 and prepare massifquant do function

    o Fix the bug in rawMat,xcmsRaw method (issue #58).
    o Prepare the "do" function for massifquant.

commit 5a505865868ae409ea01a1be81741ee1a0c8b009
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 20 14:09:17 2016 +0200

    Add .processHistory slot to xcmsSet

    o Add .processHistory slot, ProcessHistory class and functionality to
      track processing steps.
    o Add unit tests for subsetting, splitting and concatenating of xcmsSet
      objects checking that .processHistory slot is processed correctly.
    o Add showError method for xcmsSet objects that lists eventual errors
      during the feature detection step.
    o This addresses discussions in issue #55.

commit 5313459da83183f6f24576f03fe3ebd62b024a43
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Sep 19 13:16:02 2016 +0200

    Add argument stopOnError to xcmsSet function

    o Add argument stopOnError to xcmsSet to enable feature detection in all
      provided files without stopping on errors. This relates to issue #55.
    o Add related documentation.

commit fb93c843fc40ee7a41ede3f1a3746d7c7e13cd46
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Wed Sep 14 10:54:18 2016 +0200

    corrected documentation

commit b228271555c2144e8d557d5b940e4a43f2753542
Merge: d9ba200 5b73c67
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Mon Sep 12 11:28:40 2016 +0200

    bug fix

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

    Conflicts:
    	NAMESPACE
    	R/AllGenerics.R
    	R/methods-xcmsRaw.R
    	inst/unitTests/runit.findPeaksCentWaveWithIsotopeROIs.R

commit ea0e449bbd7a040b4fd6d63cad3d8cb35b6df594
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Sep 12 08:37:36 2016 +0200

    Documentation fixes and code tidying

commit 330ae95620bd2ad2f15aa74066b04d5b52cd0e2c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 9 20:34:37 2016 +0200

    Add do_detectFeatures_MSW function.

commit f3fc2b4000217f728a9b7acbabcd6ffa6c280a73
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Sep 7 16:29:38 2016 +0200

    Re-organize IO functions

    o Put new IO functions into functions-IO.R

commit c812cda0cea2a06b78571b54ab5c707489eafa22
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Sep 7 14:15:02 2016 +0200

    New data import function

    o Add new readRawData function that could replace the loadRaw and
      related S4 objects; this aims to fix issue #55.
    o Start implementing do_detectFeatures_MSW.

commit 9bce991e2ed0b66289f88030e57e5db121ed8368
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 6 11:34:52 2016 +0200

    Update NEWS

commit 16ac3ddeb24f8bcecc7290d00c93a28daeb0ad27
Merge: 4f46f61 5b73c67
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 6 11:23:04 2016 +0200

    Merge branch 'devel' into xcms3

commit 4f46f61127bb7b4fee037b10b57e67a2d070cd1b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 6 11:04:52 2016 +0200

    Add .Rbuildignore and update .gitignore

commit d9ba200c61b7d6886f527b3d17ce6361edc89b2a
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Tue Sep 6 08:51:13 2016 +0200

    splitted method 'findPeaks.centWaveWithPredictedIsotopeROIs' into two more modular methods; removed parameter list and added individual parameters instead; added documentation for new methods

commit 1bea5114fcce0796bb8f98a9e624317130934d80
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Sep 5 13:53:27 2016 +0200

    Add matchedFilter benchmarking

commit 5b73c67688add8718c998763a9d9053ea2885511
Merge: 897da00 71d4d46
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon Sep 5 13:28:58 2016 +0200

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

commit 897da00d22770f3ae8d494133d3fec85ed31aaaa
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Sep 5 11:13:31 2016 +0000

    Bump version, add NEWS

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120725 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 915d8bc1c2d3c7f4ad65ac2c5474f2c055c6e2ae
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Sep 5 11:13:24 2016 +0000

    minor bug fix in unit test

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120724 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 550d3e2dfdb1fdf4dd3ca41f4eaa313a481347c6
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Sep 5 11:13:16 2016 +0000

    Bug fix in case of small m/z ranges from peak picking using centWave and bug fix regarding scantime ranges

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120723 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 73ac8a908dc445e745f0a3e3c42108621ec27750
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Sep 5 11:13:08 2016 +0000

    Added standard generic

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120722 bc3139a8-67e5-0310-9ffc-ced21a209358

commit a989bbdc350bd34b3a2606e8b982ce0bf99d2b16
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Sep 5 11:13:01 2016 +0000

    Added function findPeaks.centWaveWithPredictedIsotopeROIs for the sensitive detection of isotope peaks based on predicted isotope ROIs

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120721 bc3139a8-67e5-0310-9ffc-ced21a209358

commit b688d92f0ac223e6bc19db0140957a9b934a86aa
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Mon Sep 5 12:48:59 2016 +0200

    minor bug fix in unit test

commit 1a69592b361794376eb01c28aaa263346acc449d
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Mon Sep 5 12:40:52 2016 +0200

    Bug fix in case of small m/z ranges from peak picking using centWave and bug fix regarding scantime ranges

commit 8686fc16075ed7e2ca2b33f6c79e513b43cee92d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Sep 5 10:51:11 2016 +0200

    Update new_features vignette

commit 7b72591f03fc429d408a89d1d4f8a92e3376ec10
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Sep 5 09:59:35 2016 +0200

    Add do_detectFeatures_centWave and doc updates

    o Export do_detectFeatures_centWave.
    o Add missing roxygen2 documentations.

commit c70e5ba9edad767f6428ae441c2cba1d01de48e2
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 2 09:21:02 2016 +0200

    Switch to do_detectFeatures_matchedFilter

    o findPeaks.matchedFilter calls do_detectFeatures_matchedFilter.
    o Default for now is to use the original code (discussed in issue #52).
    o Export useOriginalCode function that allows to switch between old and
      new implementation (default is old).
    o Describe discrepancies between old and new code for matchedFilter in
      the new_features.Rmd vignette.

commit 2962d586d6505a6f09c53cf52117571f4b250a8e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Aug 31 15:05:37 2016 +0200

    Prepare all functions for issue #52

    o Implement the test function comparing the matchedFilter
      implementations.
    o Start writing roxygen documentation for the do_ functions.
    o Tidy do_ functions up.

commit 3ed5a6b9c7bae091a9ce84156bd06eadbf17df48
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Wed Aug 31 13:34:13 2016 +0200

    Added standard generic

commit 37f742eefd85a9e87a9b813516bbaa3b8d5f16ad
Merge: efdbe68 71d4d46
Author: Hendrik Treutler <htreutle@ipb-halle.de>
Date:   Wed Aug 31 09:40:24 2016 +0200

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

commit efdbe6828acc3281a907d0385d03b129cfa25f2c
Author: htreutle <htreutle@ipb-halle.de>
Date:   Wed Aug 31 09:14:38 2016 +0200

    Added function findPeaks.centWaveWithPredictedIsotopeROIs for the sensitive detection of isotope peaks based on predicted isotope ROIs

commit 1d3bb742ee0ea3e4f2b3739a59baf15574e1b1d3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Aug 29 12:30:49 2016 +0200

    Add benchmarking vignette

    o Add benchmarking vignette.

commit 7f78f064fa8397ecf2af0e9d9a30dac9fac0e37b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Aug 25 06:25:16 2016 +0200

    Fix compilation warnings in obiwarp code

    o Replace fabs with abs calls for integer variables in the C++ code of
      obiwarp that threw warnings during package compilation.

commit 8f1b40a7d0aaaa51d8dcb709c8a78984445d8857
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Aug 24 08:38:06 2016 +0200

    Add new_functionality vignette

    o Add vignette describing new and modified functionality in xcms.

commit 57b69a902c4cfd1f159c76760f6ab495f0ebb5b8
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 23 11:32:25 2016 +0200

    Export binning functions

    o Export binYonX, breaks_on_binSize, breaks_on_nBins and
      imputeLinInterpol functions.
    o Add documenation (generated by roxygen2) for these functions.
    o Extensive unit tests for all functions.
    o Add parameter noInterpolAtEnds to imputeLinInterpol (mentioned in
      issue #49).

commit fa1a0d5825c98ee939b23a3e993c359fe05f8ac3
Merge: 88ec298 71d4d46
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 23 08:29:33 2016 +0200

    Merge branch 'devel' into xcms3

commit 88ec298cce23218ac20ed1c0dabeea73204aaa12
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 23 08:24:35 2016 +0200

    Fix and improve binning functions

    o Fix breaks calculation for bins (multiplication instead of addition in
      C-function) resulting in identical break values than R's seq would.
    o Fix binYonX and imputeLinInterpol to return results identical to
      profBinM and similar (except bugs reported in issue #46).

commit 71d4d46caab55d2eadcba535771d141bf4051837
Merge: 7f9bb05 7949102
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon Aug 22 15:31:15 2016 +0200

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

commit 7f9bb0590b91346a41f2839f392d49eebfab8c34
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Aug 22 13:30:24 2016 +0000

    Temporarily disable vignette with benchmarking.

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120327 bc3139a8-67e5-0310-9ffc-ced21a209358

commit b4f020db8c5f459d36db18574619c4e34e4e0b81
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Aug 22 12:45:33 2016 +0000

    updated NEWS and bumped version

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120325 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 3625829bc0953c868f14598eec06512264ec8998
Merge: 100cedc 2fbba30
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Aug 22 12:45:25 2016 +0000

    Merge branch 'xcms3' into devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120324 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 79491025c265337f65a1be98f662aae1f4569334
Merge: b17c615 5219078
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon Aug 22 14:44:50 2016 +0200

    fix whitespace merge conflict

commit b17c615f7449a444931097a1c936b69fd1253646
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon Aug 22 14:42:34 2016 +0200

    updated NEWS and bumped version

commit 5f57f336f7c8247a341d30c5314b959a1a4a0130
Merge: 100cedc 2fbba30
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon Aug 22 14:37:09 2016 +0200

    Merge branch 'xcms3' into devel

commit 100cedc031a2e7b0b935d0d122b7ac5373b3db95
Merge: bc80d6a e429a1b
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Mon Aug 22 12:19:25 2016 +0000

    fix merge conflict in NEWS

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@120323 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 5219078a4cd3098395f081776599e52ba6769e68
Merge: bc80d6a e429a1b
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon Aug 22 14:18:49 2016 +0200

    fix merge conflict in NEWS

commit 2fbba3060dae40cd6c1fb625172fc4e68f9ef0e7
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Aug 11 09:19:41 2016 +0200

    Implement binlinbase missing value imputation

    o Separate binning and missing value imputation from profBin* methods
      into two functions: binYonX and imputeLinInterpol.
    o Unit tests to validate that results from profBin* methods and binYonX
      and imputeLinInterpol match.

commit 77345695e4aaa9210723ccd083ed7d1f3b95f710
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 9 15:05:26 2016 +0200

    Add unit test comparing profBinM

    o Unit test to compare profBinM with binYonX with support for multiple
      data sub-sets.

commit 65d34ce811bd48774db10df922d0d6c90de5638c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 9 09:51:46 2016 +0200

    Add functionality to binYonX

    o Add support for length(fromIdx) and length(toIdx) > 1: performs the
      binning for each individual sub-set and returns a list of results.
    o Add argument returnIndex, which allows to return the index of the max
      or min value within each bin in x.
    o Change behaviour of arguments fromX and toX. These are by default NA
      now and are calculated internally based on the (eventually sub-setted)
      x values. If provided they allow to manually force the bin-range to be
      the same for all potential sub-sets.
    o Update roxygen documentation, add unit tests.

commit 379038a7c424bfd20aa85e203ae96e7c8fde4634
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Aug 8 16:07:25 2016 +0200

    Implement binlin imputation for binYonX

    o Implement the binlin imputation method for missing bin values in
      the binYonX function.
    o Add corresponding unit tests and benchmarks.

commit c98934013ea9a8521972bf5ef07956130d375f6f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Aug 8 09:42:08 2016 +0200

    Unify binning functions into single C-function

    o Define a single C-level binning function as entry point from R:
      binYonX.
    o Fix logical & and | in C.
    o Add unit test for profBinLin; that fails due to the bug in profBinLin!
    o Extend some documentations.

commit 900811d5f83825df3940e38f210ce901e9fe4a2f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Aug 5 08:11:06 2016 +0200

    Add matchedFilter do_ function

    o Implement do_detectFeatures_matchedFilter (issue #35); thus far
      containing the original code from findPeaks.matchedFilter.
    o Add tests to compare results for matchedFilter.

commit 43c68cc7ca0374cfca6504ba2e6fd83f5a003ec3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Aug 4 14:43:58 2016 +0200

    max, min, sum and mean for binning function

    o binYonX supports aggregation of values within bin using min, max, sum
      and mean.
    o Add corresponding unit tests.

commit 36f612de00b42e7c39a434d24d739a2c2801db05
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Aug 4 09:41:20 2016 +0200

    Binning function allow to shift bins

    o Add argument to binning function to allow shifting bins by
      binSize/2 to simulate the profBin method (see also issue #42).
    o Add benchmarking vignette.

commit 54218b5cfb44985ebfdeb473f5adca158bcaf171
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Aug 4 07:51:46 2016 +0200

    Binning funtions return bin mid-point

    o The C-level binning functions return the bin mid-point.
    o Add unit tests for binning functions.

commit 1aa1165c12c1500458eac3203cc11aa0ef40dfa8
Merge: 75ca47a e429a1b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 2 10:00:59 2016 +0200

    Merge branch 'devel' into xcms3

commit e429a1ba876b35cdf6a7e77a5c528be8f91fb3f7
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 2 09:54:28 2016 +0200

    Fix getXcmsRaw bug reported by Aleksandr

    o Fix the bug in getXcmsRaw that would eventually not apply retention
      time correction when reading the raw data (issue #44).

commit 75ca47a33adf11ed2bddf81d5fdc2b7445e7ad10
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Aug 2 08:41:07 2016 +0200

    Binning C-function about implemented

    o Add unit tests and write (not yet exported) documentation.

commit 500509aa5851d41101485cee8dd33079e0d1f1e6
Merge: b67dc45 d8cddeb
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Aug 1 08:29:46 2016 +0200

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

commit b67dc45a54203a4acf529da5f32aaa35e143d128
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Aug 1 08:27:55 2016 +0200

    Address missing documentation warning.

    o Fix the missing [ documentation for xcmsSet (issue #43).
    o Fix two 'partial argument match' notes in R CMD check.

commit 508c09507e5a0e5ac5e5df5ca7aba57501101163
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Aug 1 07:52:16 2016 +0200

    Prepare for C-level binning functions

    o Start implementing binning utilities in C.

commit 0f5d3c423dfda64b825883d2f9e862799c10a78b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jul 28 13:41:32 2016 +0200

    Some documentation updates.

    o Some updates that (hopefully) clarify the difference between getEIC
      and rawEIC.

commit d8cddebcc8a62c304046e372ec59523d0d160b4f
Merge: d7465f6 8e6439e
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Wed Jul 27 16:25:10 2016 +0200

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

commit b7d774bd919d8596342b228c69db7f6f58da14cf
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 27 11:23:03 2016 +0200

    Fix findmzROI.

    See issue #38

commit bc80d6ab546633b771d9a4b76553bd0eae617313
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 12:57:10 2016 +0000

    Bump version

    From: Steffen Neumann <sneumann@ipb-halle.de>

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119638 bc3139a8-67e5-0310-9ffc-ced21a209358

commit d7465f657fc27b591976d16e7b173e24fc819209
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 12:57:10 2016 +0000

    Bump version

    From: Steffen Neumann <sneumann@ipb-halle.de>

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119638 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 0976bd26e5defa62bf548a530eb16516325a71a3
Merge: acc52a4 e1d915d
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 12:57:02 2016 +0000

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

    From: Steffen Neumann <sneumann@ipb-halle.de>

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119637 bc3139a8-67e5-0310-9ffc-ced21a209358

commit a68d6cac8b51b42e94914e3e7b471dc2fa8560ed
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 12:57:02 2016 +0000

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

    From: Steffen Neumann <sneumann@ipb-halle.de>

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119637 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 8e6439e1a6b88df86c6c99c10ed309ab83f99ffb
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Jul 26 14:55:54 2016 +0200

    Bump version

commit 3a40d763d105846c5b0cc235929fe0934c026269
Merge: acc52a4 e1d915d
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Jul 26 10:50:47 2016 +0200

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

commit e1d915d74272b556e9ba61ad6455403ab8c75fea
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jul 26 10:10:22 2016 +0200

    Update NEWS file.

commit ef488cf0cc03e8d2a323c14fb4286b2d08db14d6
Merge: f8aaddc 1fbabb9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jul 26 09:53:19 2016 +0200

    Merge branch 'xcms3' into devel

commit f8aaddcae90146f34da495ea1472f33f18fb17f7
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jul 26 09:52:36 2016 +0200

    Add readme.org to .gitignore

commit e537216f5075f9739c9e851cfd08a9e4a8138ae3
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 07:16:21 2016 +0000

    Use BiocParallel for parallel processing

    o Use bplapply in getXcmsRaw.
    o Deprecate xcmsPapply.
    o Update documentations to include BPPARAM argument.
    o Import from BiocGenerics and Biobase, remove the definitions of
      phenoData and phenoData<- generics.
    o Import from graphics, stats etc to fix 'R CMD check' warnings.

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119633 bc3139a8-67e5-0310-9ffc-ced21a209358

commit c43e37a7890de080d4ce1b200695a6bbb979014a
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 07:16:11 2016 +0000

    findPeaks and fillPeaks using BiocParallel

    o Add xcmsSet2 function and fillPeaks.chrom2 method that use
      BiocParallel instead of manual parallel processing setup.
    o Add a unit test comparing the results.

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119632 bc3139a8-67e5-0310-9ffc-ced21a209358

commit db566567149f571bcc459b10e5215324bef5fbc4
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 07:16:02 2016 +0000

    Added some uncommitted mzTab stuff

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119631 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 115d8fd7560b592fd963282fefb96adbf68b4c55
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue Jul 26 07:15:55 2016 +0000

    fixed merge conflict

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@119630 bc3139a8-67e5-0310-9ffc-ced21a209358

commit c3bbb074a6817f6825dda2d740fc149a9f2c46f4
Merge: 55dfbb2 e81b590
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Jul 26 09:12:37 2016 +0200

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

commit 55dfbb2d639817b1f51bf4fabaa69281a1add4e3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 18 14:41:57 2016 +0200

    Use BiocParallel for parallel processing

    o Use bplapply in getXcmsRaw.
    o Deprecate xcmsPapply.
    o Update documentations to include BPPARAM argument.
    o Import from BiocGenerics and Biobase, remove the definitions of
      phenoData and phenoData<- generics.
    o Import from graphics, stats etc to fix 'R CMD check' warnings.

commit 74d32385367baf7dcb0880486c6f2794e7c2f05a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 18 13:27:56 2016 +0200

    findPeaks and fillPeaks using BiocParallel

    o Add xcmsSet2 function and fillPeaks.chrom2 method that use
      BiocParallel instead of manual parallel processing setup.
    o Add a unit test comparing the results.

commit 7cd59c562406eecac77d15ed05bf9d4629c4a0a0
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue May 17 00:20:39 2016 +0200

    Added some uncommitted mzTab stuff

commit 458fb021a0bf6d5ad3efd88da40475bae01ce8a3
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue Jul 26 09:09:12 2016 +0200

    fixed merge conflict

commit 1fbabb9783ef3e144ab9a8dee3aaad6f505a24c9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 25 15:17:28 2016 +0200

    Add centWave do_function.

    + Implement the do_detectFeatures_centWave function.
    + Add unit test for do_detectFeatures_centWave.
    + Code reformatting.

commit 72f8d6d69fb9b41f77ad6875a40766bbaa429b07
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jul 22 09:02:45 2016 +0200

    Move packages from Suggests to Imports

    + Move packages multtest, MassSpecWavelet and RANN from DESCRIPTION's
      Suggests to Imports field (issue #34).
    + Fix warning message in findPeaksPar.

commit 6da19f05041ab245f3cd83d04148c2d664b007f6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jul 21 10:37:21 2016 +0200

    Fix R CMD check warnings and notes (#32)

    + Move generics from CleanData.R to AllGenerics.R, methods to
      methods-xcmsRaw.R
    + Remove all DUP = FALSE from the .C calls as they are ignored anyways.
    + Fix bug in fillPeaksChromPar using an index i that does not exist.
    + Fix bug in fillPeaksChromPar referring to variable 'object' that does
      not exist.
    + Fix bug call in group.nearest to undefined variable coreList (change
      to scoreList).
    + Move all deprecated functions to Deprecated.R.

commit 623c6fdc6700f894fbfb8fa192ba86e200234953
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jul 21 10:17:57 2016 +0200

    Refactoring for xcmsEIC and xcmsFragments done.

commit 09d92f2fc2c2b371c2fc496cf4de87802acdc9b9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jul 21 09:36:08 2016 +0200

    Refactor xcmsRaw R source files.

    + Split methods/functions for xcmsRaw into respective files.
    + Put all generics into AllGenerics.R

commit 6cbe43599ae919b11bfee0de9b6887484c022c00
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jul 21 06:45:47 2016 +0200

    Done with refactoring of xcmsSet R files

    + Moved all generic method definitions for xcmsSet and xcmsRaw into
      AllGenerics.R.
    + Moved all(?) xcmsSet methods into methods-xcmsSet.R.
    + Moved all xcmsSet functions into functions-xcmsSet.R.
    + Reverted the doRUnit.R file.

commit a4d09a15aab9fc0e1d9d957ed5709d263d927c93
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jul 20 07:45:56 2016 +0200

    Add updateObject method for xcmsSet

    + Add updateObject and validity method for xcmsSet along with
      corresponding unit tests.
    + Internal cleanup: move class definitions to DataClasses.R, use
      roxygen2 to create the Collate field in DESCRIPTION.

commit e0d4e36a6db8ffd7a8d6c7753307cc39a33d2355
Merge: 55817bd e81b590
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jul 19 08:39:07 2016 +0200

    Merge branch 'devel' into xcms3

commit e81b590fd2596829103798e5d8b19e2fdfde2018
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 18 14:41:57 2016 +0200

    Use BiocParallel for parallel processing

    o Use bplapply in getXcmsRaw.
    o Deprecate xcmsPapply.
    o Update documentations to include BPPARAM argument.
    o Import from BiocGenerics and Biobase, remove the definitions of
      phenoData and phenoData<- generics.
    o Import from graphics, stats etc to fix 'R CMD check' warnings.

commit c57175f33fc13bfed929530345145edcdcb1849a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 18 13:27:56 2016 +0200

    findPeaks and fillPeaks using BiocParallel

    o Add xcmsSet2 function and fillPeaks.chrom2 method that use
      BiocParallel instead of manual parallel processing setup.
    o Add a unit test comparing the results.

commit 55817bd32eb2bae345737d16a24883e527474347
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 18 13:27:56 2016 +0200

    findPeaks and fillPeaks using BiocParallel

    o Add xcmsSet2 function and fillPeaks.chrom2 method that use
      BiocParallel instead of manual parallel processing setup.
    o Add a unit test comparing the results.

commit e01074465062a674af92f0e2704073a11899dd1f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jul 18 09:04:01 2016 +0200

    Add readme.org file.

commit fcc1feb555bf6007b0ca2d37bc8f3b6635b40a9d
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue May 17 07:41:19 2016 +0000

    Add NEWS and bump version

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@117572 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 2c5e8aa4b2ec61dc9c3a121281625830c72879ff
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue May 17 07:41:13 2016 +0000

    Added some uncommitted mzTab stuff

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@117571 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 48931274f4fd638c8123ed01f10250f0b066f2e4
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue May 17 07:41:06 2016 +0000

    First go at mzTab export

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@117570 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 0b11cc3eb8b0e879b2f4ba35c514eb71906b6f85
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue May 17 07:37:54 2016 +0200

    Add NEWS and bump version

commit 9535218aaf8e52bcd361f1c912375854104e7e76
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Tue May 17 00:20:39 2016 +0200

    Added some uncommitted mzTab stuff

commit 89ff2dbf642d5a786c8efc3bee0fcc9467933d15
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Mon May 16 23:37:04 2016 +0200

    First go at mzTab export

commit f900b6144c5eb0bbf8ccf4faee5f691861270f1e
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Sun May 15 21:30:54 2016 +0000

    The raw CDF/mzXML/mzData/mzML is assumed to have scans sorted by m/z.
    Instead of throwing an "m/z sort assumption violated !" error,
    the data is re-read and on-demand sorted by m/z.

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@117517 bc3139a8-67e5-0310-9ffc-ced21a209358

commit 7b38c2d610f66a1fee9d9330119f2b9c04fdf20e
Merge: 23c01d7 f9be4f4
Author: s.neumann <s.neumann@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Sun May 15 21:30:46 2016 +0000

    Merge branch 'fixmzsortassumption' into devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@117516 bc3139a8-67e5-0310-9ffc-ced21a209358

commit f9be4f4f23c49f56074670658bc9665e093c8f83
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date:   Fri Apr 1 14:09:29 2016 +0200

    Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)

From: Steffen Neumann <sneumann@ipb-halle.de>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms@125964 bc3139a8-67e5-0310-9ffc-ced21a209358
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10 changes: 7 additions & 3 deletions DESCRIPTION
View file
Expand Up @@ -15,7 +15,8 @@ Depends:
mzR (>= 1.1.6),
BiocGenerics,
ProtGenerics,
Biobase
Biobase,
MSnbase (>= 2.1.4)
Imports:
lattice,
RColorBrewer,
Expand All @@ -24,8 +25,7 @@ Imports:
multtest,
MassSpecWavelet (>= 1.5.2),
BiocParallel,
S4Vectors,
MSnbase (>= 2.1.4)
S4Vectors
Suggests:
BiocStyle,
knitr (>= 1.1.0),
Expand Down Expand Up @@ -59,19 +59,23 @@ Collate:
'fastMatch.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'
'functions-xcmsFragments.R'
'functions-xcmsRaw.R'
'functions-xcmsSet.R'
'init.R'
'matchpeaks.R'
'methods-IO.R'
'methods-MsFeatureData.R'
'methods-OnDiskMSnExp.R'
'methods-Params.R'
'methods-ProcessHistory.R'
'methods-XCMSnExp.R'
'methods-netCdfSource.R'
'methods-rampSource.R'
'methods-xcmsEIC.R'
Expand Down
54 changes: 46 additions & 8 deletions NAMESPACE
View file
Expand Up @@ -12,8 +12,8 @@ importFrom("plyr", "rbind.fill")
import("RColorBrewer")
import("BiocParallel")

importClassesFrom("S4Vectors", "Rle")
importFrom("S4Vectors", "split", "Rle")
importClassesFrom("S4Vectors", "Rle", "DataFrame")
importFrom("S4Vectors", "split", "Rle", "DataFrame")

## Additional imports proposed by R CMD check:
importFrom("graphics", "abline", "barplot", "close.screen", "hist",
Expand All @@ -40,7 +40,10 @@ importFrom("MassSpecWavelet", "peakDetectionCWT", "tuneInPeakInfo")
importClassesFrom("MSnbase", "MSnExp", "pSet", "OnDiskMSnExp")
importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile",
"filterFile", "filterMsLevel", "msLevel", "scanIndex",
"spectra", "impute", "isCentroided", "polarity")
"spectra", "impute", "isCentroided", "polarity", "[", "bin",
"clean", "featureNames", "filterAcquisitionNum", "filterMz",
"filterRt", "normalize", "pickPeaks", "removePeaks",
"removeReporters", "smooth", "trimMz")
importFrom("MSnbase", "as.data.frame.Spectrum")

export(
Expand Down Expand Up @@ -186,16 +189,16 @@ export(
"do_detectFeatures_centWaveWithPredIsoROIs",
"do_detectFeatures_addPredIsoROIs",
"imputeLinInterpol",
"useOriginalCode"
"useOriginalCode",
"setAs"
)

## New methods
## New analysis methods
exportMethods(
"showError",
"detectFeatures"
)


## New Param classes
exportClasses(
"CentWaveParam",
Expand Down Expand Up @@ -290,12 +293,47 @@ exportMethods(
"mzIntervalExtension",
"mzIntervalExtension<-",
"polarity",
"polarity<-"
"polarity<-",
"rtime",
"mz",
"intensity"
)
## Param class functions
export("CentWaveParam", "MatchedFilterParam", "MassifquantParam", "MSWParam",
"CentWavePredIsoParam")
## Param class methods.

## New Classes
## exportClasses("XCMSnSet")
exportClasses("XCMSnExp", "MsFeatureData", "ProcessHistory", "XProcessHistory")
## New methods for these classes
exportMethods("hasDetectedFeatures",
"hasAlignedFeatures",
"hasAdjustedRtime",
"adjustedRtime",
"adjustedRtime<-",
"featureGroups",
"featureGroups<-",
"features",
"features<-",
"processHistory",
"fileIndex",
"processDate",
"processInfo",
"processParam",
"processType",
"bin",
"clean",
"filterAcquisitionNum",
"filterFile",
"filterMsLevel",
"filterMz",
"filterRt",
"normalize",
"pickPeaks",
"removePeaks",
"smooth",
"dropAdjustedRtime",
"dropFeatureGroups",
"dropFeatures",
"spectra"
)
39 changes: 37 additions & 2 deletions R/AllGenerics.R
View file
Expand Up @@ -5,6 +5,11 @@
setGeneric("absent", function(object, class, minfrac) standardGeneric("absent"))
setGeneric("addParams", function(object, ...) standardGeneric("addParams"))
setGeneric("addParams<-", function(object, value) standardGeneric("addParams<-"))
setGeneric("addProcessHistory", function(object, ...)
standardGeneric("addProcessHistory"))
setGeneric("adjustedRtime", function(object, ...) standardGeneric("adjustedRtime"))
setGeneric("adjustedRtime<-", function(object, value)
standardGeneric("adjustedRtime<-"))
setGeneric("ampTh", function(object, ...) standardGeneric("ampTh"))
setGeneric("ampTh<-", function(object, value) standardGeneric("ampTh<-"))
setGeneric("AutoLockMass", function(object) standardGeneric("AutoLockMass"))
Expand Down Expand Up @@ -36,8 +41,22 @@ setGeneric("detectFeatures", function(object, param, ...)
setGeneric("diffreport", function(object, ...) standardGeneric("diffreport"))
setGeneric("distance", function(object, ...) standardGeneric("distance"))
setGeneric("distance<-", function(object, value) standardGeneric("distance<-"))
setGeneric("dropAdjustedRtime", function(object, ...)
standardGeneric("dropAdjustedRtime"))
setGeneric("dropFeatureGroups", function(object, ...)
standardGeneric("dropFeatureGroups"))
setGeneric("dropFeatures", function(object, ...)
standardGeneric("dropFeatures"))

## F
setGeneric("features", function(object, ...) standardGeneric("features"))
setGeneric("features<-", function(object, value)
standardGeneric("features<-"))
setGeneric("featureGroups", function(object, ...) standardGeneric("featureGroups"))
setGeneric("featureGroups<-", function(object, value)
standardGeneric("featureGroups<-"))
setGeneric("fileIndex", function(object) standardGeneric("fileIndex"))
setGeneric("fileIndex<-", function(object, value) standardGeneric("fileIndex<-"))
setGeneric("filepaths", function(object) standardGeneric("filepaths"))
setGeneric("filepaths<-", function(object, value) standardGeneric("filepaths<-"))
setGeneric("fillPeaks.chrom", function(object, ...)
Expand Down Expand Up @@ -97,6 +116,13 @@ setGeneric("groupval", function(object, ...) standardGeneric("groupval"))

## H
setGeneric("hasMSn", function(object, ...) standardGeneric("hasMSn"))
setGeneric("hasAdjustedRtime", function(object, ...)
standardGeneric("hasAdjustedRtime"))
setGeneric("hasAlignedFeatures", function(object, ...)
standardGeneric("hasAlignedFeatures"))
setGeneric("hasDetectedFeatures", function(object, ...)
standardGeneric("hasDetectedFeatures"))


## I
setGeneric("image", function(x, ...) standardGeneric("image"))
Expand Down Expand Up @@ -172,6 +198,16 @@ setGeneric("ppm<-", function(object, value) standardGeneric("ppm<-"))
setGeneric("prefilter", function(object, ...) standardGeneric("prefilter"))
setGeneric("prefilter<-", function(object, value) standardGeneric("prefilter<-"))
setGeneric("present", function(object, class, minfrac) standardGeneric("present"))
setGeneric("processDate", function(object, ...) standardGeneric("processDate"))
setGeneric("processDate<-", function(object, value) standardGeneric("processDate<-"))
setGeneric("processInfo", function(object, ...) standardGeneric("processInfo"))
setGeneric("processInfo<-", function(object, value) standardGeneric("processInfo<-"))
setGeneric("processParam", function(object, ...) standardGeneric("processParam"))
setGeneric("processParam<-", function(object, value)
standardGeneric("processParam<-"))
setGeneric("processType", function(object, ...) standardGeneric("processType"))
setGeneric("processType<-", function(object, value) standardGeneric("processType<-"))
setGeneric("processHistory", function(object, ...) standardGeneric("processHistory"))
setGeneric("profinfo", function(object) standardGeneric("profinfo"))
setGeneric("profinfo<-", function(object, value) standardGeneric("profinfo<-"))
setGeneric("profMat", function(object, ...) standardGeneric("profMat"))
Expand Down Expand Up @@ -212,7 +248,7 @@ setGeneric("scales", function(object, ...) standardGeneric("scales"))
setGeneric("scales<-", function(object, value) standardGeneric("scales<-"))
setGeneric("scanrange", function(object, ...) standardGeneric("scanrange"))
setGeneric("scanrange<-", function(object, value) standardGeneric("scanrange<-"))
setGeneric("sigma", function(object, ...) standardGeneric("sigma"))
setGeneric("sigma")
setGeneric("sigma<-", function(object, value) standardGeneric("sigma<-"))
setGeneric("showError", function(object, ...) standardGeneric("showError"))
setGeneric("snthresh", function(object, ...) standardGeneric("snthresh"))
Expand Down Expand Up @@ -264,4 +300,3 @@ setGeneric("write.mzQuantML", function(object, ...) standardGeneric("write.mzQua

## X
setGeneric("xcmsSource", function(object, ...) standardGeneric("xcmsSource"))

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