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commit d3f47ca69474af4913ad8d1cc0cfe9420011ddda
Author: jotsetung <[email protected]>
Date:   Wed Aug 9 08:40:08 2017 +0200

    Add BiocStyle package to xcms-direct-injection vignette

commit 0aba7270a9fdeae76c8ad409c6cfe702cf3bbb56
Author: jotsetung <[email protected]>
Date:   Wed Aug 9 08:18:27 2017 +0200

    Replace xcmsDirect.Rnw vignette with rmarkdown version

commit 31e1e389529913bcb06e8a5ab88328557681617b
Author: jotsetung <[email protected]>
Date:   Tue Aug 8 09:23:17 2017 +0200

    Add calibrate,XCMSnExp method

    - Add calibrate,XCMSnExp method (issue #199).
    - Add related unit tests and documentation.
    - Add a warning if peaks are not sorted by mz in calibrate,xcmsSet (issue #200).

commit 02cfd24c757557f3c32908390af9cec342c92847
Author: jotsetung <[email protected]>
Date:   Fri Aug 4 15:24:51 2017 +0200

    Update the plotChromPeakDensity function

    - plotChromPeakDensity allows now to either simulate correspondence based on
      provided settings, or to visualize correspondence results.
    - Fixed problems in plotChromPeakDensity function when cex, bg or other
      point-specific parameters were passed.
    - Increase the argument n for the density function in the peak density
      correspondence analysis by 2.

commit 3814110b76afa62458a012ce4f92787ab6bbb0c6
Author: jotsetung <[email protected]>
Date:   Fri Aug 4 13:17:30 2017 +0200

    Add arguments mz and rt to featureDefinitions

    - Add arguments mz and rt to featureDefinitions,XCMSnExp that enable to extract
      features for the specified rt / m/z range.
    - Add related documentation and unit tests.

commit 84cfdc2071425efb8cbe3dd1d3ce47792c4abdd2
Author: jotsetung <[email protected]>
Date:   Fri Aug 4 11:20:00 2017 +0200

    Add parameter main to plotChromPeakDensity function

commit d113ff3826dd6e9e9b89e050f3023f6ed4f5b0bf
Author: jotsetung <[email protected]>
Date:   Fri Aug 4 09:14:06 2017 +0200

    Clean xcmsDirect.Rnw vignette

commit d38dfa0536b37dd605f7fb374fa4163fa09951bf
Author: jotsetung <[email protected]>
Date:   Fri Jul 28 19:08:02 2017 +0200

    Fix issue #194

    - Ensure raw data objects are subsetted correctly if scanrange is provided.
    - Ensure that the profile matrices are correctly expanded to match their number
      of rows.

commit 03784d5fe6f2b684c5793308115938135969c8de
Author: jotsetung <[email protected]>
Date:   Fri Jul 28 08:30:22 2017 +0200

    Tentative fix for issue #196

    - In obiwarp for OnDiskMSnExp objects: remove the check that ensures that the
      profile matrices of the files to be aligned have to have the same
      dimension. That would require all files to have the same number of scans,
      which does not have to be the case.

commit fea13e212d96c8aaa864eb078b6b8c4f15fc7ace
Author: jotsetung <[email protected]>
Date:   Thu Jul 27 08:17:13 2017 +0200

    Bump version and update NEWS

commit fc15e26c6ad1d9ea7d2295b974d7bd1401cded52
Merge: 515b008 27e525c
Author: jotsetung <[email protected]>
Date:   Thu Jul 27 08:11:06 2017 +0200

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

commit 515b008104858809cd952866129d32da86446698
Author: jotsetung <[email protected]>
Date:   Thu Jul 27 08:05:15 2017 +0200

    Export phenoDataFromPaths function (issue #195)

    - Export the phenoDataFromPaths function to enable the old way to define the
      pheno data from the folder structure in which the files are located.
    - Add related documentation and unit test.

commit 27e525c5c76407e97a93ef997e7d22fbfd18cf4d
Merge: 1a3144a 4c22c3c
Author: Steffen Neumann <[email protected]>
Date:   Fri Jul 21 21:07:52 2017 +0200

    Merge branch 'biocdevel' into devel

commit 1a3144aafc7f8a99575398d5c7d8d3ff0ae6870f
Author: jotsetung <[email protected]>
Date:   Fri Jul 21 06:55:18 2017 +0200

    Documentation tidying.

commit f7825ada4f743ff83ea71669b888d7b1c42d47fd
Author: jotsetung <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Jul 14 09:30:23 2017 +0200

    Fix unit test to work with recent change in MSnbase

commit 9c18189766d59ab91a51f8e840a54b2832ea1259
Author: jotsetung <[email protected]>
Date:   Wed Jul 12 16:06:14 2017 +0200

    Some example performance tuning

commit 741073f6f56aa8ee29ca370b751827b5844ebe1a
Author: jotsetung <[email protected]>
Date:   Wed Jul 12 15:05:19 2017 +0200

    Fix bracket errors

commit 80a47b4d43e5eedadd98446f0392d6a6b6b36dc4
Author: jotsetung <[email protected]>
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 <[email protected]>
Date:   Wed Jul 12 10:36:42 2017 +0200

    Small fixes to the adjustDriftWithModel function

commit 02ebe57154eadf18d22745d5f7ab49fb849d5b34
Author: jotsetung <[email protected]>
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 <[email protected]>
Date:   Tue Jul 11 13:03:42 2017 +0200

    Add plotChromPeaks function (issue #154)

commit 7aa5ef0add5391e10b237f33bc36fde934b595f0
Author: jotsetung <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Fri Jun 16 13:18:19 2017 +0200

    Merge branch 'devel' into xcms3

commit 1b1e42a1d39efeabba6e9acf52bf9b74c33d6937
Author: jotsetung <[email protected]>
Date:   Fri Jun 16 13:16:42 2017 +0200

    Remove Chromatogram class

commit 710a8f9d44f3e330fe0072bf02cc9ac8548bf120
Merge: 7ef7059 056dd82
Author: Steffen Neumann <[email protected]>
Date:   Fri Jun 16 07:25:02 2017 +0200

    Merge branch 'biocdevel' into devel

commit bcac6ab7afad578085d3a83a8a911812c35cf79a
Author: jotsetung <[email protected]>
Date:   Thu Jun 15 10:19:01 2017 +0200

    Tune unit tests and vignettes #187

commit 7ef70598754cffc9e896ddb3358f62471e0d16cb
Author: jotsetung <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Tue Jun 6 12:42:12 2017 +0200

    Merge branch 'biocdevel' into devel

commit 3d03ef5433aca18593e4fc4ee126ca41dbf753a3
Merge: bafb6de 8c1220e
Author: Johannes Rainer <[email protected]>
Date:   Tue Jun 6 10:54:35 2017 +0200

    Merge pull request #185 from sneumann/issue184

    Fix issue #184

commit 8c1220eaf7f866572e726b11baaa7672c514c237
Author: jotsetung <[email protected]>
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 <[email protected]>
Date:   Wed May 31 13:04:34 2017 +0200

    Fix some more typos and tidy roxygen text

commit 5249622a585b8bea916c14a0683a158dd7210a2f
Merge: ffc9e39 54cc415
Author: jotsetung <[email protected]>
Date:   Wed May 31 12:45:50 2017 +0200

    Merge branch 'devel' into xcms3

commit ffc9e39dd8570fa51e9c4abd1b99864bdd25b7fd
Author: jotsetung <[email protected]>
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 <[email protected]>
Date:   Wed May 31 10:53:52 2017 +0200

    Merge pull request #183 from stanstrup/patch-6

    typos

commit f9bbe4287ca6f1560e33fccaad63842b58d57dfd
Author: Jan Stanstrup <[email protected]>
Date:   Wed May 31 10:51:34 2017 +0200

    typos

commit aabdf5c29daddd60aae2c7b12512dcf1f6d5bc1c
Merge: 4dfbc01 13f69c8
Author: Steffen Neumann <[email protected]>
Date:   Sun May 28 18:56:31 2017 +0200

    Merge branch 'biocdevel' into devel

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

    Fix issue #180

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

    Update NEWS.

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

    Merge branch 'devel' into xcms3

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

    Merge pull request #178 from stanstrup/patch-4

    scanrange was collapsed when the adjusted range was reported.

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

    scanrange was collapsed when the adjusted range was reported.

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

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

    Fix for issue #173

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

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

    Fix for issue #175

    - Disable original xcms-preprocessing vignette.

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

    Add extractMsData method (issue #120)

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

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

    Fix for bug introduced into plotChromPeakDensity

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

    Add Jan Stanstrup's fix also to the plotChromPeakDensity function

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

    Update news.

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

    Merge branch 'devel' into xcms3

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

    Fix problem with merge from Jan Stanstrup

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

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

    Merge pull request #162 from stanstrup/patch-5

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

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

    Remove un-needed functions from functions-XCMSnExp.R

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

    Merge branch 'biocdevel' into devel

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

    Add plotChromPeakDensity function (issue #171)

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

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

    Add new clean,Chromatogram method

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

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

    Fixes to the extractChromatograms method

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

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

    extractChromatograms extracts multiple ranges

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

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

    Fix bug in plotChromatogram

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

    Ensure plotChromatogram doesn't break if no data available

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

    Add plotChromatogram and highlightChromPeaks functions

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

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

    Fix validation method for CentWaveParam if roiList is provided

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

    Merge branch 'biocdevel' into devel

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

    Merge branch 'xcms3' into devel

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

    Update date

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

    Avoid fillPeaks using deprecated API (issue #163)

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

commit 60ff5957cf9ef6a7729710eb2fdb823209fa8d62
Author: Jan Stanstrup <[email protected]>
Date:   Tue Apr 11 11:01:47 2017 +0200

    additional fixes for #160

commit 959004a09888b236111bc0ef5a9f829a5558c174
Author: Jan Stanstrup <[email protected]>
Date:   Tue Apr 11 10:57:25 2017 +0200

    devel patch for # 160

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

    Fix possible memory problem in obiwarp (issue #159)

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

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

    Update documentation of fillPeaks.chrom

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

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

    Clean up imports and dependencies

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

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

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

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

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

    Add parameter "filled" to featureValues

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

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

    Merge branch 'biocdevel' into devel

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

    Updates to the vignette

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

    Add the plotAdjustedRtime function (issue #141)

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

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

    Support predefined peak group matrix for peak groups alignment

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

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

    Add peakGroupsMatrix slot to PeakGroupsParam class

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

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

    Remove private 'isSeizmo' massifquant function.

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

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

    Add adjustRtimePeakGroups function (issue #147)

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

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

    Use feature IDs as rownames in featureValues and featureDefinitions

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

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

    Add filterRt,Chromatogram method

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

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

    Ensure correct ordering of values in Chromatogram constructor

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

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

    Change order of alignment and correspondence in XCMSnExp,show

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

    Fix unordered adjusted retention times in peakGroups

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

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

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

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

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

    Merge branch 'devel' into xcms3

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

    Show warning if order of adjusted retention time is not increasing

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

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

    Merge branch 'biocdevel' into devel

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

    Avoid multiple/nested parallel processing

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

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

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

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

    Remove debug centWave version debug message

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

    Extend new_functionality vignette.

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

    Add fillChromPeaks for matchedFilter peak detection

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

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

    Remove commented old matchedFilter test functions.

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

    Ensure XCMSnExp compatibility for single spectrum MS data

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

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

    Support peak filling for direct infusion data

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

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

    Extend show method for XCMSnExp

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

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

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

    Add featureValues method for XCMSnExp

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

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

    Add dropFilledChromPeaks method

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

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

    Add @filled slot for XCMSnExp to xcmsSet conversion

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

    Add fillChromPeaks method and FillChromPeaksParam class

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

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

    o Remove debug messages from xcmsSet.

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

    Add modified centWave function and various fixes

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

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

    Merge branch 'devel' into xcms3

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

    Update NEWS

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

    Fix for issues #118 #133 #134

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

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

    Merge branch 'biocdevel' into devel

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

    Add columne "is_filled" to chromPeaks matrix

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

    Add findChromPeaks for XCMSnExp objects (issue #128)

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

    Rename parentMz in Chromatogram to precursorMz

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

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

    spectra,XCMSnExp returning adjusted rtime (issue #129)

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

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

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

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

    Rename methods, functions and objects (issue #126)

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

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

    Ensure memory cleanup in parallel findPeaks for xcmsSet

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

    Minor changes to Chromatogram

    o Don't export Chromatogram.

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

    Add Chromatogram class

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

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

    Merge branch 'biocdevel' into devel

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

    Bump version and update NEWS.

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

    Fix issue #124

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

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

    Bump version.

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

    Small internal changes.

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

    Small code cleanup.

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

    Update NEWS.

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

    Merge branch 'devel' into xcms3

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

    Fix unit test error on R-3.2.3

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

    filterRt filtering by default on adjusted rt if available

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

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

    rtime,XCMSnExp reports by default adjusted rt

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

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

    Add groupval,XCMSnExp method (issue #114)

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

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

    Add adjustRtime,XCMSnExp,ObiwarpParam (issue #119)

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

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

    Tentative fix for issue #118

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

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

    Add ObiwarpParam class (issue #119)

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

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

    Implement profMat method for XCMSnExp and OnDiskMSnExp

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

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

    Use do_adjustRtime_featureGroups in retcor.peakgroups

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

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

    Add adjustRtime,XCMSnExp,FeatureGroupsParam method

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

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

    Add FeatureGroupsParam object (issue #112)

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

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

    Add documentation and unit test for do_adjustRtime_featureGroups

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

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

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

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

    Add the do_adjustRtime_featureGroups function

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

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

    Remove commented code.

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

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

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

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

    Add NearestFeaturesParam class (issue #108)

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

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

    Fix warnings in group.nearest (issue #109)

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

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

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

    Add do_groupFeatures_nearest function (issue #103)

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

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

    Add do_groupFeatures_nearest function (issue #103)

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

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

    Add groupFeatures,XCMSnExp,MzClustParam (issue #107)

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

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

    Add MzClustParam class and smaller bug fixes

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

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

    Fix order issue (issue #180 in MSnbase)

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

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

    Add do_groupFeatures_mzClust function (issue #103)

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

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

    Add groupFeatures,XCMSnExp,FeatureDensityParam method

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

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

    Add FeatureDensityParam class (issue #105)

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

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

    Parallel version of the do_groupFeatures_density implemented

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

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

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

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

    Add do_groupFeatures_density function

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

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

    Bump version and adapt NEWS

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

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

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

    Merge branch 'biocdevel' into devel

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

    Removed , in DESCRIPTION

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

    Add spectrum,XCMSnExp method and increase method robustness

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

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

    Fix issue #102

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

    Fix issue #91.

    o Replay the changes made by Jan Stanstrup.

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

    Fix issue #98

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

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

    Add bySample parameter to features,XCMSnExp

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

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

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

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

    Update NEWS.

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

    Improve fix for issue #99

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

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

    Method to coerce XCMSnExp to xcmsSet

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

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

    Fix issue #101

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

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

    Add filterRt method for XCMSnExp

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

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

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

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

    Add bySample argument to adjustedRtime,XCMSnExp method

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

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

    Add bySample argument to adjustedRtime,XCMSnExp method

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

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

    Add mz, intensity and rtime methods for XCMSnExp

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

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

    Use drop* methods to remove preprocessing results

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

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

    Add sort method option

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

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

    Fix failed execution of unit tests

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

    Add drop methods

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

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

    Merge branch 'devel' into xcms3

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

    Implement filterMz method for XCMSnExp

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

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

    Fix problem reading MS2-only files.

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

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

    Implement some of the methods inherited from OnDiskMSnExp

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

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

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

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

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

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

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

    added deepCopy to avoid corrupting the original object

    #76

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

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

    Code cleanup

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

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

    Extend show method for XCMSnExp objects.

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

    Enable XCMSnExp as return object in detectFeatures

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

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

    Export the ProcessHistory and XProcessHistory classes

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

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

    Implement the detectFeatures method for CentWavePredIsoParam

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

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

    Add rtime,XCMSnExp method

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

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

    Add XCMSnExp class

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

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

    Add MsFeatureData class

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

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

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

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

    Merge branch 'stanstrup-patch-3' into devel

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

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

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

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

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

    adapted manpage for plotQC

    From: Steffen Neumann <[email protected]>

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

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

    merged xcms3 branch, added return value to plotQC()

    From: Steffen Neumann <[email protected]>

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

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

    adapted manpage for plotQC

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

    merged xcms3 branch, added return value to plotQC()

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

    added deepCopy to avoid corrupting the original object

    #76

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

    Merge branch 'devel' into xcms3

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

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

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

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

    Merge branch 'stanstrup-patch-2'

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

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

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

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

    Merge fix and bump version

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

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

    Merge remote-tracking branch 'sneumann/devel'

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

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

    Add CentWavePredIsoParam class

    o Add CentWavePredIsoParam class, documentation and unit tests.

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

    Add centWaveWithPresIsoROIs core API function

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

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

    Merge branch 'devel' into xcms3

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

    Fix wrong sample indexing in getEIC,xcmsSet

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

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

    Start implementing the do function for withAddIsotopes

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

    More informative warning.

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

    change profStepPad to use new binning functions

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

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

    Update new_functionality vignette to new BiocStyle

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

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

    Finish unit test tuning

    o Reduce processing time in the remaining unit tests.

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

    Unit test tuning

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

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

    Fix vignettes and tune unit tests

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

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

    Merge pull request #88 from Treutler/xcms3

    implemented function "do_predictIsotopeROIs" (issue #82)

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

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

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

    Add MSW detectFeatures method

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

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

    Add massifquant detectFeatures method

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

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

    Add XProcessHistory class

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

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

    Just some comments

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

    Add MassifquantParam class

    o Add a MassifquantParam class (issue #84).

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

    Add warning if data is not in centroid mode for centWave

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

    Add documentation for detectFeatures centWave and matchedFilter

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

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

    Implement MatchedFilterParam and detectFeatures method

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

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

    Add detectFeatures method for MSnExp and OnDiskMSnExp objects

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

commit e464617e26015c18f53303226e678adb9e70299b
Author: jotsetun…
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@sneumann
sneumann committed Aug 9, 2017
1 parent d2b7b8c commit 8d2c6b7
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Showing 27 changed files with 1,494 additions and 601 deletions.
4 changes: 2 additions & 2 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: xcms
Version: 2.99.5
Date: 2017-07-14
Version: 2.99.6
Date: 2017-08-09
Title: LC/MS and GC/MS Data Analysis
Author: Colin A. Smith <[email protected]>,
Ralf Tautenhahn <[email protected]>,
Expand Down
11 changes: 7 additions & 4 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,8 @@ export(
"xcmsRaw",
"xcmsSet",
"xcmsFragments",
"xcmsPapply"
"xcmsPapply",
"phenoDataFromPaths"
)

S3method(plot, xcmsEIC)
Expand Down Expand Up @@ -212,7 +213,8 @@ export(
"highlightChromPeaks",
"plotChromPeakDensity",
"plotChromPeaks",
"plotChromPeakImage"
"plotChromPeakImage",
"isCalibrated"
)

## New analysis methods
Expand All @@ -236,7 +238,8 @@ exportClasses(
"PeakGroupsParam",
"ObiwarpParam",
"GenericParam",
"FillChromPeaksParam"
"FillChromPeaksParam",
"CalibrantMassParam"
)
## Param methods
exportMethods(
Expand Down Expand Up @@ -386,7 +389,7 @@ exportMethods(
export("CentWaveParam", "MatchedFilterParam", "MassifquantParam", "MSWParam",
"CentWavePredIsoParam", "PeakDensityParam", "MzClustParam",
"NearestPeaksParam", "PeakGroupsParam", "ObiwarpParam", "GenericParam",
"FillChromPeaksParam")
"FillChromPeaksParam", "CalibrantMassParam")
## Param class methods.

## New Classes
Expand Down
118 changes: 117 additions & 1 deletion R/DataClasses.R
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Original file line number Diff line number Diff line change
Expand Up @@ -187,12 +187,14 @@ setClass("xcmsPeaks", contains = "matrix")
.PROCSTEP.PEAK.GROUPING <- "Peak grouping"
.PROCSTEP.RTIME.CORRECTION <- "Retention time correction"
.PROCSTEP.PEAK.FILLING <- "Missing peak filling"
.PROCSTEP.CALIBRATION <- "Calibration"
.PROCSTEPS <- c(
.PROCSTEP.UNKNOWN,
.PROCSTEP.PEAK.DETECTION,
.PROCSTEP.PEAK.GROUPING,
.PROCSTEP.RTIME.CORRECTION,
.PROCSTEP.PEAK.FILLING
.PROCSTEP.PEAK.FILLING,
.PROCSTEP.CALIBRATION
)

############################################################
Expand Down Expand Up @@ -2405,3 +2407,117 @@ setClass("XCMSnExp",
}
)

#' @aliases mz,CalibrantMassParam
#'
#' @title Calibrant mass based calibration of chromatgraphic peaks
#'
#' @description Calibrate peaks using mz values of known masses/calibrants.
#' mz values of identified peaks are adjusted based on peaks that are close
#' to the provided mz values. See details below for more information.
#'
#' @param mz a `numeric` or `list` of `numeric` vectors with reference mz
#' values. If a `numeric` vector is provided, this is used for each sample
#' in the `XCMSnExp` object. If a `list` is provided, it's length has to be
#' equal to the number of samples in the experiment.
#'
#' @param mzabs `numeric(1)` the absolute error/deviation for matching peaks to
#' calibrants (in Da).
#'
#' @param mzppm `numeric(1)` the relative error for matching peaks to calibrants
#' in ppm (parts per million).
#'
#' @param neighbors `integer(1)` with the maximal number of peaks within the
#' permitted distance to the calibrants that are considered. Among these the
#' mz value of the peak with the largest intensity is used in the
#' calibration function estimation.
#'
#' @param method `character(1)` defining the method that should be used to
#' estimate the calibration function. Can be `"shift"`, `"linear"` (default)
#' or `"edgeshift"`.
#'
#' @details The method does first identify peaks that are close to the provided
#' mz values and, given that there difference to the calibrants is smaller
#' than the user provided cut off (based on arguments `mzabs` and `mzppm`),
#' their mz values are replaced with the provided mz values. The mz values
#' of all other peaks are either globally shifted (for `method = "shift"`
#' or estimated by a linear model through all calibrants.
#' Peaks are considered close to a calibrant mz if the difference between
#' the calibrant and its mz is `<= mzabs + mz * mzppm /1e6`.
#'
#' **Adjustment methods**: adjustment function/factor is estimated using
#' the difference between calibrant and peak mz values only for peaks
#' that are close enough to the calibrants. The availabel methods are:
#' * `shift`: shifts the m/z of each peak by a global factor which
#' corresponds to the average difference between peak mz and calibrant mz.
#' * `linear`: fits a linear model throught the differences between
#' calibrant and peak mz values and adjusts the mz values of all peaks
#' using this.
#' * `edgeshift`: performs same adjustment as `linear` for peaks that are
#' within the mz range of the calibrants and shift outside of it.
#'
#' For more information, details and examples refer to the
#' *xcms-direct-injection* vignette.
#'
#' @note `CalibrantMassParam` classes don't have exported getter or setter
#' methods.
#'
#' @return For `CalibrantMassParam`: a `CalibrantMassParam` instance.
#' For `calibrate`: an [XCMSnExp] object with chromatographic peaks being
#' calibrated. **Be aware** that the actual raw mz values are not (yet)
#' calibrated, but **only** the identified chromatographic peaks.
#'
#' @author Joachim Bargsten, Johannes Rainer
#'
#' @md
#'
#' @rdname calibrate-calibrant-mass
setClass("CalibrantMassParam",
slots = c(
mz = "list",
mzabs = "numeric",
mzppm = "numeric",
neighbors = "integer",
method = "character"
),
contains = c("Param"),
prototype = prototype(
mz = list(),
mzabs = 0.0001,
mzppm = 5,
neighbors = 3L,
method = "linear"
),
validity = function(object) {
msg <- character()
if (length(object@mz)) {
is_num <- vapply(object@mz, FUN = is.numeric,
FUN.VALUE = logical(1), USE.NAMES = FALSE)
if (any(!is_num))
msg <- c(msg, paste0("'mz' has to be a list of numeric",
" vectors"))
is_unsorted <- vapply(object@mz, FUN = is.unsorted,
FUN.VALUE = logical(1),
USE.NAMES = FALSE)
if (any(is_unsorted))
msg <- c(msg, paste0("the mz values in 'mz' have to be ",
"increasingly ordered"))
}
if (length(object@mzppm) != 1 | any(object@mzppm < 0))
msg <- c(msg, paste0("'mzppm' has to be positive numeric",
" of length 1."))
if (length(object@mzabs) != 1 | any(object@mzabs < 0))
msg <- c(msg, paste0("'mzabs' has to be positive numeric",
" of length 1."))
if (length(object@neighbors) != 1 | any(object@neighbors <= 0))
msg <- c(msg, paste0("'neighbors' has to be positive integer",
" of length 1."))
if (length(object@method) != 1)
msg <- c(msg, paste0("'method' has to be of length 1."))
if (!all(object@method %in% c("linear", "shift", "edgeshift")))
msg <- c(msg, paste0("'method' should be one of 'linear'",
", 'shift' or 'edgeshift'."))
if (length(msg))
msg
else
TRUE
})
3 changes: 2 additions & 1 deletion R/do_groupChromPeaks-functions.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,8 @@ do_groupChromPeaks_density <- function(peaks, sampleGroups,

densFrom <- rtRange[1] - 3 * bw
densTo <- rtRange[2] + 3 * bw
densN <- max(512, 2^(ceiling(log2(diff(rtRange) / (bw / 2)))))
## Increase the number of sampling points for the density distribution.
densN <- max(512, 2 * 2^(ceiling(log2(diff(rtRange) / (bw / 2)))))
endIdx <- 0
num <- 0
gcount <- integer(nSampleGroups)
Expand Down
9 changes: 6 additions & 3 deletions R/functions-OnDiskMSnExp.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,13 @@ findChromPeaks_Spectrum_list <- function(x, method = "centWave", param, rt) {
if (is.unsorted(rt))
stop("Spectra are not ordered by retention time!")
mzs <- lapply(x, mz)
vals_per_spect <- lengths(mzs, FALSE)
procDat <- date()
res <- do.call(method, args = c(list(mz = unlist(mzs,
use.names = FALSE),
int = unlist(lapply(x, intensity),
use.names = FALSE),
valsPerSpect = lengths(mzs, FALSE),
valsPerSpect = vals_per_spect,
scantime = rt),
as(param, "list")))
## Ensure that we call the garbage collector to eventually clean unused stuff
Expand Down Expand Up @@ -301,8 +302,10 @@ findPeaks_MSW_Spectrum_list <- function(x, method = "MSW", param) {
mzvals <- length(mzs)
cntrVals <- length(cntrPr$profMat)
curVals <- length(curP$profMat)
if ((mzvals * valscantime1) != cntrVals | (mzvals * valscantime2) != curVals
| cntrVals != curVals)
if ((mzvals * valscantime1) != cntrVals | (mzvals * valscantime2) != curVals)
## Here the question is if we REALLY need to have the same numbers
## of values in both. This caused the problems in issue #196
## | cntrVals != curVals)
stop("Dimensions of profile matrices of files ",
basename(fileNames(cntr)), " and ", basename(fileNames(z)),
" do not match!")
Expand Down
31 changes: 31 additions & 0 deletions R/functions-Params.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -301,3 +301,34 @@ FillChromPeaksParam <- function(expandMz = 0, expandRt = 0, ppm = 0) {
return(new("FillChromPeaksParam", expandMz = expandMz, expandRt = expandRt,
ppm = ppm))
}


#' @return The `CalibrantMassParam` function returns an instance of
#' the `CalibrantMassParam` class with all settings and properties set.
#'
#' @md
#'
#' @rdname calibrate-calibrant-mass
CalibrantMassParam <- function(mz = list(), mzabs = 0.0001, mzppm = 5,
neighbors = 3, method = "linear") {
if (!is.list(mz))
mz <- list(mz)
mz <- lapply(mz, sort)
new("CalibrantMassParam", mz = mz, mzabs = mzabs, mzppm = mzppm,
neighbors = as.integer(neighbors), method = method)
}

.mzabs <- function(x)
x@mzabs

.mzppm <- function(x)
x@mzppm

.neighbors <- function(x)
x@neighbors

.method <- function(x)
x@method

.mz <- function(x)
x@mz
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