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NEWS
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Changes in version 3.99.3
----------------------
- Small fixes in the *direct injection* vignette.
- Add parameter `isolationWindowTargetMz` to the `chromatogram` function for
`MsExperiment` and `XcmsExperiment` to ensure MS2 chromatographic data is
extracted from the MS2 spectra containing fragments of the compound of
interest.
Changes in version 3.99.2
----------------------
- Add the `xmse` data set representing an `XcmsExperiment` object.
- Update the *compounding* vignette to use the new objects.
- Add `loadXcmsData` to load test data objects (and fix/update paths).
- Add `groupFeatures` methods for `XcmsExperiment`.
- Fix issue in `featureArea` for `XcmsExperiment`.
- Update main vignette to use and describe the new data objects.
- Add `findChromPeaksIsolationWindow` method for `MsExperiment` and
`XcmsExperiment`.
- Make `reconstructChromPeakSpectra` a method.
- Add `reconstructChromPeakSpectra` implementation for `XcmsExperiment`.
- Add `filterIsolationWindow` for `MsExperiment` and `XcmsExperiment` to filter
spectra (and eventually chromatographic peaks) based on the isolation window.
- Update the LC-MS/MS vignette adding also an example how to deisotope SWATH
MS2 spectra.
Changes in version 3.99.1
----------------------
- `featureSummary` and `overlappingFeatures` gain support for `XcmsExperiment`.
- Fix in `featureChromatograms` to ensure a valid object is returned.
Changes in version 3.99.0
----------------------
- Add `XcmsExperiment` and support for `MsExperiment`/`Spectra`: add all
functionality for a full xcms processing on a `MsExperiment` object.
- Fix issue in `refineChromPeaks` with `MergeNeighboringPeaksParam` where a
wrong apex position was considered in the evaluation whether candidate peaks
should be merged (would only happen for merging of > 2 candidate peaks).
- Re-write the `reconstructChromPeakSpectra` for DIA data analysis to fix an
issue with chromatographic peaks in overlapping SWATH isolation windows and
generally to improve performance.
Changes in version 3.21.5
---------------------
- Fix issue in `chromatogram` after filtering a result object (issue #511).
Changes in version 3.21.4
---------------------
- Move multtest from Suggests to Imports in dependencies
Changes in version 3.21.3
---------------------
- Only fixes in the long running tests
Changes in version 3.21.2
---------------------
Changes in version 3.21.1
---------------------
- Fix error with `fillChromPeaks` on sparse data (many empty spectra) and peak
detection performed with `MatchedFilterParam` (issue #653).
- Update to newer function names in the `rgl` package (issue #654).
Changes in version 3.19.2
----------------------
- Update/expand documentation for the `firstBaselineCheck` parameter of
centWave.
Changes in version 3.19.1
----------------------
- Update documentation to reference updates in MassSpecWavelet package.
Changes in version 3.17.6
----------------------
- Rewrite code to subset features and chromatographic peaks. This results in a
perfomance improvement for `filterFile` and similar functions.
- Add parameter `expandMz` to `featureChromatograms`
(https://github.com/sneumann/xcms/issues/612).
Changes in version 3.17.5
----------------------
- Change the way the m/z value for a chromatographic peak is determined by
centWave: if a ROI contains more than one peak for one scan (spectrum) an
intensity-weighted m/z is reported for that scan. The m/z of the
chromatographic peak is then calculated based on these reported m/z values for
each scan (spectrum). In the original version the mean m/z for a scan was
reported instead. As a result, m/z values of chromatographic peaks are now
slightly different but are expected to be more accurate. See
https://github.com/sneumann/xcms/issues/590 for more details.
Changes in version 3.17.4
----------------------
- Add `transformIntensity` method.
- Fix issue when calling `chromPeakSpectra` or `featureSpectra` on an object
that contains also files with only MS1 spectra
(https://github.com/sneumann/xcms/issues/603).
Changes in version 3.17.2
----------------------
- Use mzML instead of mzData files in testing and vignettes,
since mzR drop mzData reading and msdata package will drop mzData files as well
Changes in version 3.17.1
----------------------
- Fix bug in feature grouping by EIC correlation that would return a
non-symmetric similarity matrix.
- Fix error message from issue [584](https://github.com/sneumann/xcms/issues/584).
Changes in version 3.15.5
----------------------
- Disable testing on windows i386, providing some speedup
- Disable parallel processing on Windows, causing an issue in testthat on BioC build check
Changes in version 3.15.4
----------------------
- Fix in `plot` with `type = "XIC"` to plot an empty plot if no data is present.
- Skip re-indexing of peaks to features if not necessary. This results in
performance improvements for MS1 only data.
Changes in version 3.15.3
----------------------
- Add `manualFeatures` allowing to manually define and add features to an
`XCMSnExp` object.
- Add `plotChromatogramsOverlay` function to support plotting of multiple EICs
from the same sample into the same plot (eventually stacked).
- Add feature grouping by EIC similarity: `EicSimilarityParam`.
- Import `compareChromatograms` from `MSnbase`.
- Add feature grouping by similar retention time: `SimilarRtimeParams.
- Add feature grouping by similarity of feature abundances across samples:
`AbundanceSimilarityParam`.
- Add feature grouping methodology based on `MsFeatures`.
Changes in version 3.15.2
----------------------
- Fix LC-MS/MS vignette.
Changes in version 3.15.1
----------------------
- Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus.
Changes in version 3.13.8
----------------------
- Fix plotQC() for XCMSnExp objects
Changes in version 3.13.7
----------------------
- Add `featureArea` function to extract the m/z-rt region for features.
- Fix `featureSpectra` function.
- Re-add the LC-MS/MS vignette.
- Feature: plotQC() supports XCMSnExp objects now
Changes in version 3.13.6
----------------------
- Fix issue #545: skip second centWave run with CentWavePredIsoParam in regions
of interest with undefined peak boundaries/scan ranges.
- Temporarily remove the LC-MS/MS vignette (until MsBackendMgf is added to
Bioconductor).
Changes in version 3.13.5
----------------------
- Add `filterChromPeaks` method to filter chromatographic peaks in a
`XChromatogram` or `XChromatograms` object.
- Add `filterChromPeaks` method for `XCMSnExp` (issue #541).
- Support return of `Spectra` objects by `chromPeakSpectra`, `featureSpectra`
and `reconstructChromPeakSpectra`.
- Support extraction of MS1 spectra with `chromPeakSpectra`.
- Support extraction of the spectrum with the largest total signal or largest
base peak signal in `chromPeakSpectra`.
- Add support for extraction of spectra for selected/individual peaks/features
using the `peaks` and `features` parameter in `chromPeakSpectra` and
`featureSpectra`, respectively.
Changes in version 3.13.4
----------------------
- Import `Param` object from `ProtGenerics`.
- Import `filterIntensity`, `normalize` and `alignRt` for `Chromatogram` and
`MChromatograms` from `MSnbase`.
Changes in version 3.13.3
----------------------
- `align,Chromatogram` gains new method `"none"` which will only keep values
with identical retention times. For `method = "matchRtime"` the (much faster)
matching function `closest` from the `MsCoreUtils` package is used.
- Method `correlate,Chromatogram` gains parameter `useIntensitiesAbove` to
perform the correlation only with values larger than this threshold
(avoiding thus high correlation because of many 0-values).
- Add method `filterIntensity,Chromatogram` that allows to filter a chromatogram
object keeping only data points with an intensity above a user provided
threshold.
Changes in version 3.13.2
----------------------
- Add new function `manualChromPeaks` allowing to manually add and integrate
chromatographic peaks.
Changes in version 3.13.1
----------------------
- Support subsetting of `XChromatograms` with `drop = FALSE`.
Changes in version 3.11.8
----------------------
- Disable parallel processing in vignettes.
Changes in version 3.11.7
----------------------
- More efficient splitting data per file especially for larger data sets.
- Disable parallel processing in examples.
Changes in version 3.11.6
----------------------
- Add `FilterIntensityParam` to filter chromatographic peaks on intensity
(issue #502).
- Add `estimatePrecursorIntensity` function to determine the precursor intensity
for MS2 spectra from the neighboring MS1 spectra.
Changes in version 3.11.4
----------------------
- Change from `Spectra` and `Chromatograms` to `MSpectra` and `MChromatograms`
from MSnbase version >= 2.15.3.
Changes in version 3.11.3
----------------------
- `reconstructChromPeakSpectra`: report also polarity and `precusorIntensity`.
- `reconstructChromPeakSpectra`: ensure a retention time is reported for
reconstructed MS2 spectra (issue #485).
- Change default for `expandRt` to `0` in `reconstructChromPeakSpectra`.
- Fix error in `refineChromPeaks,MergeNeighboringPeaksParam` if no peaks found
to be merged.
Changes in version 3.11.2
----------------------
- Add `fillChromPeaks,ChromPeakAreaParam` to base the area from which missing
peak data should be filled-in on the actually detected chromatographic peaks
of a feature.
- Potential fix for issue #481: function should no longer throw an error because
retention times are of length 0.
- More efficient splitting of processing which should increase the speed of
the findChromPeaks, refineChromPeaks, reconstructChromPeakSpectra and
chromPeakSpectra calls.
Changes in version 3.11.1
----------------------
- Fix issue #471: conversion from `XCMSnExp` to `xcmsSet` looses phenodata
(thanks to Andris Jankevics for reporting and providing a solution).
- Add `normalize` method for `Chromatogram` and `Chromatograms` objects.
- `featureChromatograms` gets new parameter `n` and `value` to extract EICs
only from the top n samples with highest intensities.
- `filterFile` gets new parameter `keepFeatures` to support retaining
correspondence results even if a data set is filtered by file.
- Export the virtual `Param` class.
- Add filterColumnsIntensityAbove method for Chromatograms object that allows
to select columns (samples) of an Chromatograms object for which intensities
of its chromatographic data are higher than a threshold.
- Add removeIntensity method for Chromatogram, Chromatograms, XChromatogram
and XChromatograms objects allowing to *remove* intensities based on different
criteria.
- Add correlate method for Chromatograms allowing to correlate multiple
chromatograms with each other.
Changes in version 3.9.4
----------------------
- Fix issue in centWave which skips peak detection depending on minimum
peakwidth (issue #445): add parameter `extendLengthMSW` in `CentWaveParam`.
Thanks to William Kumler for contributing the fix.
- Tentatively reduce memory requirements in `fillChromPeaks`.
- Fix issue #467 for fillPeaks() of an xcmsSet converted from an XCMSnSet
Changes in version 3.9.3
----------------------
- Move multtest from Imports to Suggests to avoid duplicated method definition
for plot (issue #459).
- Add support for peak filling from MS level > 1 to fillChromPeaks.
- featureValues gains parameter msLevel to extract feature values for features
of all, or from a specific MS level.
- refineChromPeaks supports different MS levels.
- Added support to perform correspondence analysis on MS level > 1 and add the
respective results to already present feature definitions.
- hasChromPeaks and hasFeatures gain parameter msLevel to check for presence of
chromatographic peaks or features from a specific MS level.
Changes in version 3.9.2
----------------------
- Fix featureChromatograms and chromatograms on a XCMSnExp object with features:
features can be duplicated across rows (EICs).
- findChromPeaks: add parameter `add` to allow several rounds of peak detections
on the same object.
- Small performance enhancement in fillChromPeaks.
- Better support for MS > 1 data in fillChromPeaks: skip MS level 2 spectra for
filling in.
- Add refineChromPeaks for XChromatogram and XChromatograms objects.
- Add groupOverlaps function to group arbitrary ranges.
- Add quantify,XCMSnExp object to quantify an XCMSnExp into a
SummarizedExperiment.
- Fine-tune MergeNeighboringPeaks peak refinement method: the average of the
3 data points between candidate peaks is used to evaluate whether the peaks
should be merged making the approach more robust against outliers. In
addition, an ion chromatogram for candidate peaks is extracted with an m/z
range expanded depending on the expandMz and ppm setting ensuring that low
intensity data points between candidate peaks are not missed out (because
their m/z might be slightly shifted on ToF instruments). The mzmin and mzmax
of the merged peak represents also the minimum and maximum m/z of all data
points in that extracted ion chromatogram.
Changes in version 3.9.1
----------------------
- Fix problem of not shown/plotted peak positions in plotChromPeakSpectra
for experiments in which peaks were not detected in the first sample(s).
- Add method *from_to* to missing value imputation method `imputeRowMinRand`.
- Show warning in findChromPeaks if empty spectra are detected.
- Add refineChromPeaks method and CleanPeaksParam class to allow removal of
chromatographic peaks exceeding a user-definable maximal peak width.
- Add MergeNeighboringPeaksParam for refineChromPeaks to allow merging of
chromatographic peaks close in m/z and retention time with a signal between
them higher than a certain threshold (issue #414).
- Fix misspelled parameter `mzd` in LC-MS/MS vignette.
Changes in version 3.7.5
----------------------
- Remove xcmsMSn vignette (based on old xcms).
Changes in version 3.7.4
----------------------
- mzClust correspondence analysis: check and fix missing values in column mz of
the peaks matrix (issue #416).
Changes in version 3.7.3
----------------------
- plot type = "XIC" on an XCMSnExp object will draw rectangles indicating the
identified chromatographic peaks.
- Add a vignette describing LC-MS/MS data analysis with xcms.
Changes in version 3.7.2
----------------------
- Fix documentation (issue #401).
- Add support for SWATH data analysis.
Changes in version 3.7.1
----------------------
- Add correlate method for Chromatogram objects.
- Add parameter lwd to plotAdjustedRtime.
- Add align method for Chromatogram objects.
- Add findChromPeaksIsolationWindow to enable chromatographic peak detection
in isolation windows.
- Fix issue in chromPeakSpectra with method = "signal".
- chromPeakSpectra and featureSpectra return now MS2 spectra with an precursor
m/z >= mzmin, <= mzmax and retention time >= rtmin, <= rtmax.
- Improve performance of chromPeakSpectra and featureSpectra.
Changes in version 3.5.5
----------------------
- Add dirname and dirname<- methods for OnDiskMSnExp to change the path to the
raw data files.
- Add section "Subset-based alignment" to the xcms vignette to describe the
alignment possibility to perform alignments based on a subset of samples
(e.g. QC samples).
Changes in version 3.5.4
----------------------
- Fix problem in featureChromatograms with include = "feature_only" that could
return a non-valid object.
- Ensure that XCMSnExp objects are updated if necessary in all analysis methods.
Changes in version 3.5.3
----------------------
- Fix unit tests.
Changes in version 3.5.2
----------------------
- Small changes in fillChromPeaks,XCMSnExp to reduce memory demand.
- Fix issue #359.
- Fix issue #360: rawEIC skipped last scan/spectrum if rtrange was provided.
- filterMsLevel keeps now chromatographic peaks and feature definitions from the
specified MS levels (issue #362).
- Fix bug in `xcmsRaw` that leads to a netCDF error message (issue #363).
- Add parameter msLevel to chromPeaks for XCMSnExp objects.
- Add chromPeakData to allow adding arbitrary annotation to chromatographic
peaks.
- Change default of parameter value in featureValues from value = "index" to
value = "into".
- Add parameter isFilledColumn to chromPeaks allowing the old behaviour to
include the is_filled column in the chromatographic peak matrix.
Changes in version 3.5.1
----------------------
- Fix issue #349.
- Add updateObject function for XCMSnExp objects (issue #347).
- Add dropFilledChromPeaks methods for XChromatogram and XChromatograms objects.
- Add parameter filled = FALSE to chromatogram and featureChromatograms
functions.
- Fix matchedFilter peak detection problems with empty spectra (issue #325).
- featureChromatograms extracts by default only chromatographic peaks associated
with a feature.
- chromatogram,XCMSnExp extracts an XChromatogram containing also
chromatographic peaks and feature definitions.
- Add featureValues method for XChromatograms objects (issue #336).
- Add correspondence analysis (peak grouping) for chromatographic data (for now
only with PeakDensity method; issue #336).
- Add featureDefinitions slot to XChromatograms object and related accessor
methods.
- Add subset alignment option subsetAdjust = "average" to adjust left-out
samples (blanks or simply non-subset samples) based on an interpolation from
the results of the previous and subsequent subset sample.
- Add parameter subsetAdjust to PeakGroupsParam allowing to switch between
different methods to adjust samples left out in the alignment process.
- Alignment based on a sample subset for the peak groups method (issue #335):
sample subset can be defined with the subset parameter, samples not included
in the subset will be aligned based on the adjusted retention times of the
closest sample in the subset.
- Add findChromPeaks,XChromatograms (issue #332).
- Add processHistory,XChromatograms.
- Add plot,XChromatograms method with automatic peak highlighting (issue #334).
- Add hasChromPeaks,XChromatograms method.
- Add XChromatograms class with constructor function and coercing method.
- Add hasChromPeaks,XChromatogram method.
- Add filterRt,XChromatogram, filterMz,XChromatogram.
- Add plot,XChromatogram function supporting of highlighting/drawing identified
chromatographic peaks.
- findChromPeaks,Chromatogram returns an XChromatogram object (issue #329).
- Add chromPeaks,XChromatogram (issue #329).
- Add XChromatogram object (issue #329).
- Fix higlightChromPeaks with type = "polygon": peak filling represents now the
full detected peak and is no longer cut by the provided rt.
- Add argument peakIds to highlightChromPeaks allowing to specify the IDs of
peaks to be highlighted.
- Add example on clustering of base peak chromatograms to the vignette (issue
#328).
- Small fix in the vignette (issue #327).
- Add parameter groupval to exportMetaboAnalyst (issue #296).
- Fix bug in show,XCMSnExp that would throw an error if no process history is
present.
Changes in version 3.3.6
----------------------
- Add type = "polygon" to highlightChromPeaks allowing to fill the actual
signal area of identified chromatographic peaks.
Changes in version 3.3.5
----------------------
- Performance enhancement of the chromPeakSpectra and featureSpectra functions.
Changes in version 3.3.4
----------------------
- Add featureChromatograms to extract ion chromatograms for each feature.
- Add hasFilledChromPeaks function.
- Add argument skipFilled to the featureSummary function.
Changes in version 3.3.3
----------------------
- Add chromPeakSpectra and featureSpectra functions to extract MS2 spectra
for chromatographic peaks and features, respectively (issue #321).
- Fix profMat to handle also data files with empty spectra (issue #312).
- Add argument ylim to plotAdjustedRtime (issue #314).
- Add imputeRowMin and imputeRowMinRand, two simple missing value imputation
helper functions.
- Fix additional problem mentioned in issue #301 with obiwarp retention time
correction if some spectra have m/z values of `NA`.
- Fix issue #300 avoiding chromatographic peaks with rtmin > rtmax.
- Fixes for issues #291, #296.
- Add parameter 'missing' to diffreport allowing to replace NA with arbitrary
numbers.
- Add exportMetaboAnalyst function to export the feature matrix in MetaboAnalyst
format.
- Add parameter missing to featureValues allowing to specify how to handle/
report missing values.
- The chromPeaks matrix has now rownames to uniquely identify chromatographic
peaks in an experiment. Chromatographic peak IDs start with "CP" followed by
a number.
Changes in version 3.3.2
----------------------
- Add writeMSData method for XCMSnExp allowing to write mzML/mzXML files with
adjusted retention times (issue #294).
- Fix profEIC call for single-scan-peak (pull request #287 from @trljcl).
- Fix centWave avoiding that the same peak is reported multiple times if
fitgauss = TRUE is used (issue #284).
- featureSummary reports also RSD (relative standard deviations) of features
across samples (issue #286).
- Add parameters fixedMz and fixedRt to FillChromPeaksParam that allow to
increase the features' m/z and rt widths by a constant factor.
- Add option "sum" to featureValues' method parameter allowing to sum the
intensities of peaks that are assigned to the same feature in a file/sample.
Changes in version 3.3.1
----------------------
- Add overlappingFeatures function to identify overlapping or close features.
- Add support for type = "apex_within" for featureDefinitions.
- Fix a bug in fillChromPeaks that would return the integrated signal being Inf.
- Fix for issue #267: error in fillChromPeaks when the retention time of the
peaks are outside of the retention time range of certain files.
- New featureSummary function to calculate basic feature summaries (number of
samples in which peaks were found etc).
- Parameter 'type' added to plotChromPeakDensity and 'whichPeaks' to
highlightChromPeaks. Both parameters are passed to the 'type' argument
of chromPeaks.
- Parameter 'type' in chromPeaks gets additional option "apex_within" to return
chromatographic peaks that have their apex within the defined rt and/or m/z
range.
- Add functions rla and rowRla to calculate RLA (relative log abundances).
- Add peaksWithMatchedFilter to perform peak detection in chromatographic
(MRM/SRM) data (issues #277 and #278).
- Add peaksWithCentWave to perform centWave peak detection in chromatographic
(MRM/SRM) data (issue #279).
- Add findChromPeaks,Chromatogram methods for CentWaveParam and
MatchedFilterParam (issue #280).
Changes in version 3.1.3
----------------------
BUG FIXES:
- Fix misplaced parenthesis in the check for multiple spectra in
findChromPeaks,OnDiskMSnExp,MSWParam. Thanks to @RonanDaly (PR #276).
- Update link to correct metlin page in diffreport result (issue #204).
Changes in version 3.1.2
----------------------
NEW FEATURES
- Add filterFeatureDefinitions function.
BUG FIXES:
- Fix #273: better error message in case not a single feature could be defined
by groupChromPeaks.
Changes in version 3.1.1
----------------------
NEW FEATURES
- Reading raw files using xcmsSet or xcmsRaw uses now the automatic file type
detection feature from mzR.
- c function to concatenate XCMSnExp objects.
- groupnames method for XCMSnExp objects (issue #250).
BUG FIXES:
- Fix #237: findPeaks.MSW was not throwing an error if applied to multi-spectrum
MS file.
- Fix #249: quantile call in adjustRtime PeakGroups without na.rm = TRUE.
- Fix #259
Changes in version 2.99.10
----------------------
BUG FIXES:
- Fix #230: Failing vignettes on Windows.
Changes in version 2.99.9
----------------------
USER VISIBLE CHANGES:
- Chromatographic peak detection uses adjusted retention times on an aligned
XCMSnExp object (issue #213, #208).
- New parameter msLevel for processHistory,XCMSnExp.
- New parameter keepAdjustedRtime for filterMsLevel,XCMSnExp, dropChromPeaks,
XCMSnExp and dropFeatureDefinitions,XCMSnExp.
- Add parameter msLevel to chromatogram,XCMSnExp method (issue #205).
- Obiwarp alignment is now performed on one MS level and adjustment is applied
to all MS levels (issue #214).
- Add function plotMsData to plot intensity against retention time and m/z
against retention time for a MS slice in one sample.
- Add argument msLevel = 1L to extractMsData method (issue #223).
- New applyAdjustedRtime function to consolidate the alignment results, i.e.
replace the raw retention times in the XCMSnExp with the adjusted retention
times.
- [,XCMSnExp method gains argument keepAdjustedRtime to allow keeping adjusted
retention times in the sub-setting.
- Implement spectrapply,XCMSnExp to ensure returned results use adjusted
retention times (if present).
- [[,XCMSnExp method returns a Spectrum object with adjusted retention time, if
the XCMSnExp contains adjusted retention times.
- Argument 'sampleGroups' is mandatory for 'PeakDensityParam' (issue #228).
BUG FIXES:
- Fix #191: Excessive memory use in fillPeaks.
- Fix #220: peaks matrix is missing column "sample" if no peaks were found in
the first sample.
- Fix #222: findChromPeaks does not return an XCMSnExp object filtered to a
single MS level despite peak detection is performed on a single level.
- Fix problem in plotMsData causing wrong colors to be used to label the data
points.
Changes in version 2.99.8
----------------------
BUG FIXES:
- Replace xcmsMSn Rnw with Rmd vignette to fix Windows build errors.
Changes in version 2.99.7
----------------------
BUG FIXES:
- Fix #201: Warnings: 'readMSData2' is deprecated, thanks to L. Gatto.
- Merge with BioC git after transition
Changes in version 2.99.6
----------------------
NEW FEATURES:
- calibrate,XCMSnExp method that allows to calibrate chromatographic peaks.
USER VISIBLE CHANGES:
- Export phenoDataFromPaths function (issue $195).
- Add arguments mz and rt to featureDefinitions method allowing to extract
features within the specified ranges.
- Increase n for the density function call in group density-based correspondence
by 2.
- Replace xcmsDirect.Rnw with rmarkdown-based vignette using the new user
interface.
BUG FIXES:
- issue #196: removed the unnecessary requirement for same-dimension profile
matrices in adjustRtime,XCMSnExp,ObiwarpParam.
- issue #194: fixes in retcor.obiwarp: 1) subset raw data if scanrange != NULL.
2) if the mz range of the two files to be aligned differ, expand them
correctly. Depending on the profStep and the mz values/ranges the matrices
were not expanded correctly.
- Potential problems in the plotChromPeakDensity function.
Changes in version 2.99.5
----------------------
USER VISIBLE CHANGES:
- Re-enable sleep parameter in findPeaks.centWave and findPeaks.matchedFilter.
Changes in version 2.99.4
----------------------
NEW FEATURES:
- Add plotChromPeaks function to plot the definition (rt and mz range) of
detected chromatographic peaks of one file into the mz-rt plane.
- Add plotChromPeakImage function to plot the number of detected peaks along
the retention time axis per file as an image plot.
USER VISIBLE CHANGES:
- Move Chromatogram class and functionality to the MSnbase package
- Add argument msLevel to the findChromPeaks method to allow (chromatographic)
peak detection also on MS level > 1.
BUG FIXES:
- Polarity information was not read from mzXML files (issue #192).
Changes in version 2.99.3
----------------------
BUG FIXES:
- issue #188: determine file type from file content if file ending not known.
Changes in version 2.99.2
----------------------
BUG FIXES:
- issue #181: problem when isCentroided,Spectrum method returns NA because of
too few peaks in a spectrum. Fixed by checking in such cases all spectra in
the file.
- issue #184: add parameter sleep to do_groupChromPeaks_density function to be
backwards compatible with the old group.density code.
Changes in version 2.99.1
----------------------
NEW FEATURES:
- extractMsData to extract raw MS data as a data.frame (issue #120).
BUG FIXES:
- issue #175: an error is now thrown if no peak group was identified for peak
group retention time correction.
- issue #178: scanrange was collapsed when the adjusted range was reported
(pull request by Jan Stanstrup).
- issue #180: error when both parameters method and smooth are provided in the
retcor method.
Changes in version 2.99.0
----------------------
NEW FEATURES:
- plotChromatogram and highlightChromPeaks functions.
- plotChromPeakDensity function.
- clean method for Chromatogram classes.
USER VISIBLE CHANGES:
- Change default for ppm parameter in chromPeaks method to 0.
- extractChromatograms supports extraction of multiple rt and mz ranges.
- New parameter missing for extractChromatograms allowing to specify the
intensity value to be used for rts for which no signal is available within
the mz range.
- extractChromatograms returns Chromatograms of length equal to the number of
scans within the specified rt range, even if no signals are measured
(intensity values are NA).
Changes in version 1.53.1
----------------------
BUG FIXES:
- Increase parameter n for the density call in the peak density correspondence
method. This enables to separate neighboring peaks using small n (issue #161).
Thanks to Jan Stanstrup.
Changes in version 1.51.11
----------------------
NEW FEATURES:
- Parameter "filled" for featureValues (issue #157).
- Parameters "rt" and "mz" in chromPeaks method allowing to extract
chromatographic peaks from the specified ranges (issue #156).
BUG FIXES:
- Fixed possible memory problem in obiwarp (issue #159).
- Update getPeaks to use non-deprecated API (issue #163).
Changes in version 1.51.10
----------------------
NEW FEATURES:
- filterRt for Chromatogram class (issue #142).
- adjustRtimePeakGroups function (issue #147).
- adjustRtime,XCMSnExp,PeakGroupsParam and do_adjustRtime_peakGroups support
use of pre-defined matrix to perform alignment (issue #153).
- plotAdjustedRtime to visualize alignment results (issue #141).
USER VISIBLE CHANGES:
- featureDefinitions and featureValues return DataFrame and matrix with rownames
corresponding to arbitrary feature IDs (issue #148).
- New peakGroupsMatrix slot for PeakGroupsParam class (issue #153).
BUG FIXES:
- Issue #146: ensure adjusted retention times returned by the peakGroups method
to be in the same order than the raw retention times.
Changes in version 1.51.9
----------------------
NEW FEATURES:
- fillChromPeaks, dropFilledChromPeaks methods and FillChromPeaksParam class.
- featureValues method.
USER VISIBLE CHANGES:
- Extended new_functionality vignette.
- Change default backend for reading mzML files to pwiz.
BUG FIXES:
- Issue #135: fix peak signal integration for centWave.
- Issue #139: problem with expand.mz and expand.rt in fillPeaks.chrom.
- Issue #137: Error in findChromPeaks if no peaks are found.
Changes in version 1.51.8
----------------------
NEW FEATURES:
- Add Chromatogram class and extractChromatograms method.
BUG FIXES:
- Issue #118: failing unit test on Windows build machine.
- Issue #133: error with c() and xcmsSet without peaks.
- Issue #134: xcmsSet constructor endless loop.
Changes in version 1.51.7
----------------------
USER VISIBLE CHANGES:
- Major renaming of methods and classes to follow the naming convention:
- chromatographic peak (chromPeak): the peaks identified in rt dimension.
- feature: mz-rt feature, being the grouped chromatographic peaks within and
across samples.
BUG FIXES:
- Issue #127: failing unit test on Windows build machine.
Changes in version 1.51.6
----------------------
NEW FEATURES:
- groupFeatures and adjustRtime methods for XCMSnExp objects.
- New Param classes for groupFeatures and adjustRtime analysis methods: FeatureDensityParam,
MzClustParam, NearestFeaturesParam, FeatureGroupsParam and ObiwarpParam.
BUG FIXES:
- Issue #124 (filterRt,XCMSnExp returned empty object).
Changes in version 1.51.5
----------------------
NEW FEATURES:
- MsFeatureData and XCMSnExp objects.
- features, features<-, adjustedRtime, adjustedRtime<-, featureGroups,
featureGroups<-, hasAlignedFeatures, hasAdjustedRtime and hasDetectedFeatures
methods.
- dropFeatures, dropFeatureGroups and dropAdjustedRtime methods.
- filterMz, filterRt, filterFile etc implemented.
- mz, intensity and rtime methods for XCMSnExp allowing to return values grouped
by sample.
BUG FIXES:
- Issue #99 (rtrange outside of retention time range in getEIC,xcmsSet).
- Issue #101 (xcmsRaw function returns NULL if mslevel = 1 is specified).
- Issue #102 (centWave returns empty matrix if scales not OK). Thanks to J. Stanstrup.
- Issue #91 (warning instead of error if no peaks in ROI). Thanks to J. Stanstrup.
Changes in version 1.51.4
----------------------
BUG FIXES:
- added deepCopy to avoid corrupting the original object, thanks to J. Stanstrup, closes #93
Changes in version 1.51.3
----------------------
NEW FEATURES:
- binYonX binning function.
- imputeLinInterpol function providing linear interpolation of missing values.
- breaks_on_binSize and breaks_on_nBins functions to calculate breaks defining
bins.
- New vignette "new_functionality.Rmd" describing new and modified functionality
in xcms.
- Add do_detectFeatures_matchedFilter function.
- Add do_detectFeatures_centWave function.
- Add do_detectFeatures_centWaveWithPredIsoROIs function and unit test.
- Implement a new data import function.
- Add do_detectFeatures_MSW function and unit test.
- Argument stopOnError in xcmsSet function that allows to perform feature
detection on all files without stopping on errors.
- Method showError for xcmsSet objects that list all errors during feature
detection (if stopOnError = FALSE in the xcmsSet function).
- [ method to subset xcmsRaw objects by scans.
- profMat method to extract/create the profile matrix from/for an xcmsRaw.
- Add new detectFeatures methods for MSnExp and OnDiskMSnExp objects from the
MSnbase package.
- Add new CentWaveParam, MatchedFilterParam, MassifquantParam, MSWParam and
CentWavePredIsoParam parameter class to perform method dispatch in the
detectFeatures method.
- retcor.obiwarp uses the new binning methods for profile matrix generation.
- scanrange,xcmsRaw reports always a scanrange of 1 and length(object@scantime).
- scanrange,xcmsSet reports the scanrange eventually specified by the user in
the xcmsSet function.
- Fixed bug in rawMat (issue #58).
- Fix issue #60: findPeaks.massifquant always returns a xcmsPeaks object.
Changes in version 1.51.2
----------------------
USER VISIBLE CHANGES:
- As suggested by Jan Stanstrup, do not error if a centWave ROI
contains no data, closes #90
Changes in version 1.51.1
----------------------
BUG FIXES:
- Fix incorrrect indexing getEIC function reported by Will Edmands, closes #92
Changes in version 1.49.7
----------------------
BUG FIXES:
- Fix documentation warnings.
Changes in version 1.49.6
----------------------
USER VISIBLE CHANGES:
- Peak Picking function findPeaks.centWaveWithPredictedIsotopeROIs() and findPeaks.addPredictedIsotopeFeatures(),
which allow more sensitive detection of isotope features.
Changes in version 1.49.5
----------------------
USER VISIBLE CHANGES:
- Some documentation updates.
- Preparation for a new binning function
Changes in version 1.49.4
----------------------
BUG FIXES:
- Fix getXcmsRaw that would prevent retention time correction to be applied
(issue #44 reported by Aleksandr).
Changes in version 1.49.3
----------------------
NEW FEATURE:
- updateObject method for xcmsSet.
USER VISIBLE CHANGES:
- xcms uses now BiocParallel for parallel processing. All other parallel
processing functions have been deprecated.