Changes in version 4.2
Changes in version 4.2.3
- Fix for issue #755: chromatogram() with msLevel = 2L did return
empty data if parameter isolationWindowTargetMz was not specified
(or respective spectra variable was NA). By default, now, all MS2
spectra are integrated if isolationWindowTargetMz is not specified.
Changes in version 4.2.2
- Fix for issue #734: plot,MsExperiment is now working with
MsExperiment that have also MS2 Data.
Changes in version 4.2.1
- Fix in dropFeatureDefinitions() that was not correctly removing
additional metadata from gap-filled chromatographic peaks.
Changes in version 4.1
Changes in version 4.1.13
- Add parameter rtimeDifferenceThreshold to ObiwarpParam allowing to
customize the threshold used by obiwarp to determine whether gaps
are present in the sequence of retention times of a sample. This
addresses/fixes issue #739.
Changes in version 4.1.12
- Implementation of the LamaParama class and method for the
adjustRtime() function. Allowing alignment of a dataset based on
landmarks (lamas) from an external reference dataset.
- Implementation of related user-level function
matchLamasChromPeaks(), summarizeMatchLama() and plot(LamaParama)
which allows for evaluation of matching between lamas and
chromPeaks.
Changes in version 4.1.11
- Clean up of required and suggested packages and namespace imports.
- Re-creation of bundled data objects.
Changes in version 4.1.10
- Ensure backward compatibility for parameter objects that gained
additional slots.
Changes in version 4.1.9
- Fix bug in filterFeatures,PercentMissingFilter.
Changes in version 4.1.8
- Fixing issue #716: edit of .empty_chrom_peaks function so an sn
column is returned. Fixes extracting and plotting of peaks after
using manualChromPeaks
Changes in version 4.1.7
- Implementation of filterFeatures function with filter parameters:
RsdFilter, DratioFilter, PercentMissingFilter, BlankFlag. They can
be used ot filter features from XcmsResult and SummarizedExperiment
objects.
- Addition of a section in the main xcms vignette to describe how to
use it.
Changes in version 4.1.6
- Import filterSpectra from MsExperiment.
- Import breaks_ppm from MsCoreUtils.
- Update featureArea function to consider all chromatographic peaks
per feature, not only the one with the highest intensity. As a
consequence, returned m/z and rt ranges might be higher which has an
influence in featureChromatograms, EIC-based feature grouping and,
to a lesser extent also in gap-filling. Related documentation was
updated.
- Improve performance of the featureArea function (and related of the
PeakAreaParam-based gap filling).
- Add parameter ppm to PeakDensityParam to enable peak-density-based
correspondence throgh m/z-dependent bins along the m/z.
Changes in version 4.1.5
- Improve performance of the chromatogram call for XcmsExperiment
objects.
- Remove internal (not exported) normalization functions. These have
been transferred to the MetaboCoreUtils package.
- Support subsetting of XcmsExperiment with negative indices.
Changes in version 4.1.4
- Rename variable data in the vignette to faahko.
- Fix issue in adjustRtime resulting in corrupt processHistory.
- Add support to perform peakGroups alignment using pre-defined anchor
peak matrix (i.e., the numeric matrix with retention times of anchor
peaks in the samples that can be used to align these samples).
- Fix errors related to invalid Chromatogram objects extracted from
xcms results: ensure MS level in chromPeaksMatrix is integer.
- Fix definition of anchor peaks for peakGroups alignment with subset
(issue #702).
- Add filterMsLevel method for MsExperiment and XcmsExperiment.
- Ensure chunk-wise processing of Spectra (introduced with
version 1.13.2) is disabled when xcms is using its own chunk-wise
processing.
Changes in version 4.1.3
- Add parameter verboseBetaColumns to CentWaveParam to enable
calculation of additional peak quality metrics comparing the EIC to
an idealized bell curve.
Changes in version 4.1.2
- Add a param = to generic function storeResults: PlainTextParam to
save an XcmsExperiment or MsExperiment object as colleciton of plain
text files.
Changes in version 4.1.1
- Add method storeResults and one of its param =: RDataParam to save
an XcmsExperiment object as an .RData file.
Changes in version 3.99
Changes in version 3.99.6
- Add method to coerce a XcmsExperiment to a xcmsSet (issue #696).
- Support providing only mz or rt also for chromatogram,MsExperiment.
Changes in version 3.99.5
- Only mz or rt need to be provided for chromatogram.
Changes in version 3.99.4
- Add chromPeakChromatograms function to extract (EIC) chromatograms
for chromatographic peaks.
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
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 3.21.1
- 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
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
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.
Changes in version 3.15
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
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
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
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
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
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
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
Changes in version 3.1.3
- 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
- Add filterFeatureDefinitions function.
- Fix #273: better error message in case not a single feature could be
defined by groupChromPeaks.
Changes in version 3.1.1
- 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).
- 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
Changes in version 2.99.10
- Fix #230: Failing vignettes on Windows.
Changes in version 2.99.9
- 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).
- 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
- Replace xcmsMSn Rnw with Rmd vignette to fix Windows build errors.
Changes in version 2.99.7
- Fix #201: Warnings: 'readMSData2' is deprecated, thanks to L. Gatto.
- Merge with BioC git after transition
Changes in version 2.99.6
- calibrate,XCMSnExp method that allows to calibrate chromatographic
peaks.
- 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.
- 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
- Re-enable sleep parameter in findPeaks.centWave and
findPeaks.matchedFilter.
Changes in version 2.99.4
- 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.
- 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.
- Polarity information was not read from mzXML files (issue #192).
Changes in version 2.99.3
- issue #188: determine file type from file content if file ending not
known.
Changes in version 2.99.2
- 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
- extractMsData to extract raw MS data as a data.frame (issue #120).
- 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
- plotChromatogram and highlightChromPeaks functions.
- plotChromPeakDensity function.
- clean method for Chromatogram classes.
- 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
Changes in version 1.53.1
- 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
Changes in version 1.51.11
- Parameter "filled" for featureValues (issue #157).
- Parameters "rt" and "mz" in chromPeaks method allowing to extract
chromatographic peaks from the specified ranges (issue #156).
- Fixed possible memory problem in obiwarp (issue #159).
- Update getPeaks to use non-deprecated API (issue #163).
Changes in version 1.51.10
- 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).
- featureDefinitions and featureValues return DataFrame and matrix
with rownames corresponding to arbitrary feature IDs (issue #148).
- New peakGroupsMatrix slot for PeakGroupsParam class (issue #153).
- 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
- fillChromPeaks, dropFilledChromPeaks methods and FillChromPeaksParam
class.
- featureValues method.
- Extended new_functionality vignette.
- Change default backend for reading mzML files to pwiz.
- 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
- Add Chromatogram class and extractChromatograms method.
- 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
- 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.
- Issue #127: failing unit test on Windows build machine.
Changes in version 1.51.6
- groupFeatures and adjustRtime methods for XCMSnExp objects.
- New Param classes for groupFeatures and adjustRtime analysis
methods: FeatureDensityParam, MzClustParam, NearestFeaturesParam,
FeatureGroupsParam and ObiwarpParam.
- Issue #124 (filterRt,XCMSnExp returned empty object).
Changes in version 1.51.5
- 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.
- 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
- added deepCopy to avoid corrupting the original object, thanks to J.
Stanstrup, closes #93
Changes in version 1.51.3
- 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
- As suggested by Jan Stanstrup, do not error if a centWave ROI
contains no data, closes #90
Changes in version 1.51.1
- Fix incorrrect indexing getEIC function reported by Will Edmands,
closes #92
Changes in version 1.49
Changes in version 1.49.7
- Fix documentation warnings.
Changes in version 1.49.6
- Peak Picking function findPeaks.centWaveWithPredictedIsotopeROIs()
and findPeaks.addPredictedIsotopeFeatures(), which allow more
sensitive detection of isotope features.
Changes in version 1.49.5
- Some documentation updates.
- Preparation for a new binning function
Changes in version 1.49.4
- Fix getXcmsRaw that would prevent retention time correction to be
applied (issue #44 reported by Aleksandr).
Changes in version 1.49.3
- updateObject method for xcmsSet.
- xcms uses now BiocParallel for parallel processing. All other
parallel processing functions have been deprecated.
- Added missing package imports.
- Fix bug in fillPeaksChromPar referencing a non-existing variables i
and object.
- Fix bug in group.nearest: variable scoreList was mis-spelled
(coreList).
- Remove all DUP = FALSE from the .C calls as they are ignored
anyways.
- Re-organization of class, function and method definitions in
R-files.
- Use roxygen2 to manage the DESCRIPTION's collate field.
Changes in version 1.49.2
- Initial support for exporint mzTab format. Since Changes are still
to be expected, xcms:::writeMzTab() is not yet exported.
Changes in version 1.49.1
- The raw CDF/mzXML/mzData/mzML is assumed to have scans sorted by
m/z. Instead of throwing an "m/z sort assumption violated !" error,
the data is re-read and on-demand sorted by m/z.
Changes in version 1.47
Changes in version 1.47.3
- Disable parallel processing in unit tests causing a timeout on BioC
build machines
Changes in version 1.47.2
- Fix problem in getEIC on xcmsSet objects reported by Alan Smith in
issue #7 and add a RUnit test case to test for this (test.issue7 in
runit.getEIC.R).
- Changed some unnecessary warnings into messages.
Changes in version 1.47.2
- Disabled parallel processing in unit tests
- migrate dependencies from ncdf -> ncdf4
Changes in version 1.45
Changes in version 1.45.7
- Disabled Rmpi support and usage on Windows
Changes in version 1.45.6
- J. Rainer implemented a [ method that allows to subset an xcmsSet.
- Fixed a problem in split.xcmsSet that did not split the phenoData
properly. Added some details to the documentation of xcmsSet-class.
Changes in version 1.45.5
- The sampclass method for xcmsSet will now return the content of the
column "class" from the data.frame in the phenoData slot, or if not
present, the interaction of all factors (columns) of that
data.frame.
- The sampclass<- method replaces the content of the "class" column in
the phenoData data.frame. If a data.frame is submitted, the
interaction of its columns is calculated and stored into the "class"
column.
- Fixed a bug that resulted in a cryptic error message when no input
files are available to the xcmsSet function.
Changes in version 1.45.4
- Fixed a bug in the levelplot method for xcmsSet.
Changes in version 1.45.3
- xcmsSet now allows phenoData to be an AnnotatedDataFrame.
- new slots for xcmsRaw:
- mslevel: store the mslevel parameter submitted to xcmsRaw.
- scanrange: store the scanrange parameter submitted to xcmsRaw.
- new slots for xcmsSet:
- mslevel: stores the mslevel argument from the xcmsSet method.
- scanrange: to keep track of the scanrange argument of the
xcmsSet method.
- new methods for xcmsRaw:
- levelplot: similar to the image method, plots m/z vs RT with
color coded intensities.
- mslevel: returns the value for the .mslevel slot. For downstream
compatibility, this method returns NULL if the object does not
have the same named slot.
- profinfo: same functionality as the profinfo method for xcmsSet.
- scanrange: returns the value for the scanrange slot. For
downstream compatibility, this method returns NULL if the object
does not have the same named slot.
- new methods for xcmsSet:
- getXcmsRaw: returns a xcmsRaw object for one or more files in
the xcmsSet, eventually applying retention time correction etc.
- levelplot: similar to the image method, plots m/z vs RT with
color coded intensities. Allows in addition to highlight
identified peaks.
- mslevel: returns the value for the mslevel slot. For downstream
compatibility, this method returns NULL if the object does not
have the same named slot.
- profMethod: same functionality as the profMethod method of
xcmsRaw.
- profStep: same functionality as the profStep method of xcmsRaw.
- scanrange: returns the value for the scanrange slot. For
downstream compatibility, this method returns NULL if the object
does not have the same named slot.
- show method for xcmsSet updated to display also informations about
the mslevel and scanrange.
- Elaborated some documentation entries.
- rtrange and mzrange for xcmsRaw method plotEIC use by default the
full RT and m/z range.
- Added arguments "lty" and "add" to plotEIC method for xcmsRaw.
- getEIC without specifying mzrange returns the ion chromatogram for
the full m/z range (i.e. the base peak chromatogram).
- Checking if phenoData is a data.frame or AnnotatedDataFrame and
throw an error otherwise.
- xcmsSet getEIC method for water Lock mass corrected files for a
subset of files did not evaluate whether the specified files were
corrected.
Changes in version 1.45.2
- The xcms split() function now accepts factors that are shorter than
the number of samples in the xcmsSet, following more closely the
standard split() behaviour
Changes in version 1.45.1
- plotrt now allows col to be a vector of color definition, same as
the plots for retcor methods.
- Added $ method to access phenoData columns in a eSet/ExpressionSet
like manner.
- Allow to use the "parallel" package for parallel processing of the
functions xcmsSet and fillPeaks.chrom.
- Thanks to J. Rainer!
Changes in version 1.43
Changes in version 1.43.3
- Give a more verbose error message when file not found
Changes in version 1.43.2
- Use ProtGenerics, adapted xcms peaks()
Changes in version 1.43.1
- function plotQC() for plotting various QC plots on RT and m/z
Changes in version 1.41
Changes in version 1.41.1
- fix sampclass generation from phenoData if some combinations of
factors don't exist
- disable parallel code in manpages to avoid issues on BioC windows
build farm machines
Changes in version 1.39
Changes in version 1.39.6
- Massifquant reports the maximum intensity for each isotope trace
(peak). This is useful for interactive parameter optimization.
- Major memory reduction in parallel fillPeaks() thanks to Jan
Stanstrup. Now using an environment to mirror gvals to each list
item in the very large argList.
Changes in version 1.39.4
- Fixed write.cdf(), which had an intensity offset of +1, added a unit
test
Changes in version 1.39.3
- New R-devel check unload better. Lingering ramp code removed, import
from mzR. Cleaned up other errors in package check.
Changes in version 1.39.1
- Updated doubleMatrix c code to allow for larger profile matrixes
- Moved inst/doc to vignettes
Changes in version 1.37
Changes in version 1.37.6
- Introducing write.mzQuantML(xcmsSet) to export the peak list and
grouped matrix to the PSI format mzQuantML (see
http://www.psidev.info/mzquantml)
- Add Brigham Young University to LICENSE file for copyright purposes.
- Add copyright information display when running
findPeaks.massifquant() within xcmsRaw.R
- Clean and update documentation for findPeaks.massifquant-methods.Rd
- Remove unused parameters in findKalmanROIs() within xcmsRaw.R
Changes in version 1.37.5
- fixed bug in retcor.obiwarp where the scanrange of the first sample
would be checked instead of the center sample
Changes in version 1.37.4
- Skip t-test in diffreport() if one class has less than 2 samples.
Changes in version 1.37.3
- fixed bug in patternVsRowScore (group.nearest) that was introduced
by the modifications in rev 65169 and caused features to be aligned
that were far outside the given m/z and retention time windows.
Changes in version 1.37.1
- fixed fillPeaks, which 1) dropped non-standard columns and 2) failed
if nothing to do, based on patches by Tony Larson.
Changes in version 1.37.1
- Introducing msn2xcmsRaw, to allow findPeaks() on MS2 and MSn data
Changes in version 1.35
Changes in version 1.35.7
- fixed indexing bug in group.nearest, which under certain
circumstances caused all peaks in the first sample to be ignored
(reported by Tony Larson)
Changes in version 1.35.6
- Obiwarp retention time alignment error-ed if scanrange was used as a
parameter setting during xcmsSet/peak detection The method now tries
to automatically find the set scanrange and uses this range for
alignment.
Changes in version 1.35.4
- Introducing parallel fillPeaks
- Replace snow requirement with minimum R version 2.14.0
Changes in version 1.35.3
- if group.density was used with very low minfrac settings (< 0.5) it
did not return all feature groups, but only those that include
features from at least 50% of samples in a group. This limitation
was removed.
Changes in version 1.35.2
- Behind the scenes xcms now uses the xcmsSource class to read raw
data. This allows e.g. to write a class that pulls raw data from
e.g. a database
- massifquant: simplified logic structure of Tracker::claimDataIdx
resolved failure on new test case.
- massifquant: reporting features data structure compatible with
multiple sample comparison within XCMS.
Changes in version 1.35.1
- The mzData export is now much faster and uses less memory
Changes in version 1.33
Changes in version 1.33.16
- diffreport and plotEIC have a new parameter mzdec, with is the
number of decimal places of the m/z values in the EIC plot title
Changes in version 1.33.16
- Lock mass gap filler now works with netCDF lock mass function file
to find the exact times of the scans and works with the newer Waters
MS instruments.
Changes in version 1.33.15
- scanrage is now honoured in xcmsSet, also when in parallel mode
Changes in version 1.33.14
- scanrage is now honoured in xcmsRaw, and consequently also in
xcmsSet(matchedFilter), where previously it was ignored.
Changes in version 1.33.13
- write.cdf() has been fixed to write files AMDIS can read
Changes in version 1.33.12
- write.mzData adds Polarity to the file if available
Changes in version 1.33.11
- centWave uses a new method to estimate local noise which improves
detection of closely spaced peaks
- group.mzClust was failing when result had one peak
Changes in version 1.32
For more details and all changes before May 2012 please see the (now
discontinued) CHANGELOG in the source package (inst/ folder).
CHANGED BEHAVIOUR since Version 1.32:
Other Changes since Version 1.32:
- improved mzData writing, now includes MSn spectra and less verbose.
- improved netCDF writing, but not yet good enough for AMDIS
CHANGED BEHAVIOUR since Version 1.14:
- centWave may report a smaller set of peaks, due to a small bug in
the ROI algorithm some features with mass deviation > ppm were
retained.
Other Changes since Version 1.14:
- New method for grouping: an algorithm inspired by mzMine
group(method="nearest") has been implemented. It is slower than
group(method="density"). It can individually group close-eluting
peaks of very similar mass
- New method for retention time correction: The
retcor(method="obiwarp") algorithm operates on the raw data, and
thus allows to correct runs without well-behaving peak groups, or
without peak picking at all.
- fillPeaks(method="MSW") is now also available for direct infusion
spectra. The findPeaks(method="MSW") now returns several
intensities, and correctly reports mzmin and mzmax for peaks.
- centWave now uses dynamic memory allocation, needs much less memory,
and these BUF related errors should be a thing of the past.
- centWave gains an optional argument "noise", which is useful for
data that was centroided without any intensity threshold, centroids
with intensity < "noise" are omitted from ROI detection
- the fillPeaks() methods now remember which was an observed, and
which was a "filled" peak.
- For direct infusion spectra diffreport() now shows the raw peak
shapes, and also indicated "real" and "filled" peaks.
- xcmsRaw can now filter for positive/negative spectra, if the file
includes both polarities. xcmsSet() can pass the polarity to contain
positive/negative peaks only.