NEWS.md
In sneumann/xcms: LC-MS and GC-MS Data Analysis

xcms 4.1

Fix for issue #734. XIC plot is is now working with MS2 Data.

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.

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.

Clean up of required and suggested packages and namespace imports.
Re-creation of bundled data objects.

Ensure backward compatibility for parameter objects that gained additional slots.

Fix bug in filterFeatures,PercentMissingFilter.

Fixing issue #716: edit of .empty_chrom_peaks function so an sn column is returned. Fixes extracting and plotting of peaks after using manualChromPeaks

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.

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.

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.

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.

Add parameter verboseBetaColumns to CentWaveParam to enable calculation of additional peak quality metrics comparing the EIC to an idealized bell curve.

Add a param = to generic function storeResults: PlainTextParam to save an XcmsExperiment or MsExperiment object as colleciton of plain text files.

Add method storeResults and one of its param =: RDataParam to save an XcmsExperiment object as an .RData file.

xcms 3.99

Add method to coerce a XcmsExperiment to a xcmsSet (issue #696).
Support providing only mz or rt also for chromatogram,MsExperiment.

Only mz or rt need to be provided for chromatogram.

Add chromPeakChromatograms function to extract (EIC) chromatograms for chromatographic peaks.

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.

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.

featureSummary and overlappingFeatures gain support for XcmsExperiment.
Fix in featureChromatograms to ensure a valid object is returned.

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.

xcms 3.21

Fix issue in chromatogram after filtering a result object (issue #511).

Move multtest from Suggests to Imports in dependencies

Only fixes in the long running tests

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).

xcms 3.19

Update/expand documentation for the firstBaselineCheck parameter of centWave.

Update documentation to reference updates in MassSpecWavelet package.

xcms 3.17

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.

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.

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).

Use mzML instead of mzData files in testing and vignettes, since mzR drop mzData reading and msdata package will drop mzData files as well

Fix bug in feature grouping by EIC correlation that would return a non-symmetric similarity matrix.
Fix error message from issue 584.

xcms 3.15

Disable testing on windows i386, providing some speedup
Disable parallel processing on Windows, causing an issue in testthat on BioC build check

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.

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.

Fix LC-MS/MS vignette.

Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus.

xcms 3.13

Fix plotQC() for XCMSnExp objects

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

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).

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.

Import Param object from ProtGenerics.
Import filterIntensity, normalize and alignRt for Chromatogram and MChromatograms from MSnbase.

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.

Add new function manualChromPeaks allowing to manually add and integrate chromatographic peaks.

Support subsetting of XChromatograms with drop = FALSE.

xcms 3.11

Disable parallel processing in vignettes.

More efficient splitting data per file especially for larger data sets.
Disable parallel processing in examples.

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.

Change from Spectra and Chromatograms to MSpectra and MChromatograms from MSnbase version >= 2.15.3.

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.

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.

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.

xcms 3.9

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

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.

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.

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.

xcms 3.7

Remove xcmsMSn vignette (based on old xcms).

mzClust correspondence analysis: check and fix missing values in column mz of the peaks matrix (issue #416).

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.

Fix documentation (issue #401).
Add support for SWATH data analysis.

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.

xcms 3.5

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).

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.

Fix unit tests.

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.

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.

xcms 3.3

Add type = "polygon" to highlightChromPeaks allowing to fill the actual signal area of identified chromatographic peaks.

Performance enhancement of the chromPeakSpectra and featureSpectra functions.

Add featureChromatograms to extract ion chromatograms for each feature.
Add hasFilledChromPeaks function.
Add argument skipFilled to the featureSummary function.

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.

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.

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).

xcms 3.1

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).

Add filterFeatureDefinitions function.
Fix #273: better error message in case not a single feature could be defined by groupChromPeaks.

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

xcms 2.99

Fix #230: Failing vignettes on Windows.

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.

Replace xcmsMSn Rnw with Rmd vignette to fix Windows build errors.

Fix #201: Warnings: 'readMSData2' is deprecated, thanks to L. Gatto.
Merge with BioC git after transition

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.

Re-enable sleep parameter in findPeaks.centWave and findPeaks.matchedFilter.

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).

issue #188: determine file type from file content if file ending not known.

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.

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.

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).

xcms 1.53

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.

xcms 1.51

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).

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.

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.

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.

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.

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).

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.

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

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.

As suggested by Jan Stanstrup, do not error if a centWave ROI contains no data, closes #90

Fix incorrrect indexing getEIC function reported by Will Edmands, closes #92

xcms 1.49

Fix documentation warnings.

Peak Picking function findPeaks.centWaveWithPredictedIsotopeROIs() and findPeaks.addPredictedIsotopeFeatures(), which allow more sensitive detection of isotope features.

Some documentation updates.
Preparation for a new binning function

Fix getXcmsRaw that would prevent retention time correction to be applied (issue #44 reported by Aleksandr).

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.

Initial support for exporint mzTab format. Since Changes are still to be expected, xcms:::writeMzTab() is not yet exported.

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.

xcms 1.47

Disable parallel processing in unit tests causing a timeout on BioC build machines

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.

Disabled parallel processing in unit tests
migrate dependencies from ncdf -> ncdf4

xcms 1.45

Disabled Rmpi support and usage on Windows

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.

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.

Fixed a bug in the levelplot method for xcmsSet.

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.

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

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!

xcms 1.43

Give a more verbose error message when file not found

Use ProtGenerics, adapted xcms peaks()

function plotQC() for plotting various QC plots on RT and m/z

xcms 1.41

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

xcms 1.39

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.

Fixed write.cdf(), which had an intensity offset of +1, added a unit test

New R-devel check unload better. Lingering ramp code removed, import from mzR. Cleaned up other errors in package check.

Updated doubleMatrix c code to allow for larger profile matrixes
Moved inst/doc to vignettes

xcms 1.37

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

fixed bug in retcor.obiwarp where the scanrange of the first sample would be checked instead of the center sample

Skip t-test in diffreport() if one class has less than 2 samples.

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.

fixed fillPeaks, which 1) dropped non-standard columns and 2) failed if nothing to do, based on patches by Tony Larson.

Introducing msn2xcmsRaw, to allow findPeaks() on MS2 and MSn data

xcms 1.35

fixed indexing bug in group.nearest, which under certain circumstances caused all peaks in the first sample to be ignored (reported by Tony Larson)

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.

Introducing parallel fillPeaks
Replace snow requirement with minimum R version 2.14.0

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.

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.

The mzData export is now much faster and uses less memory

xcms 1.33

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

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.

scanrage is now honoured in xcmsSet, also when in parallel mode

scanrage is now honoured in xcmsRaw, and consequently also in xcmsSet(matchedFilter), where previously it was ignored.

write.cdf() has been fixed to write files AMDIS can read

write.mzData adds Polarity to the file if available

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

xcms 1.32 and before

For more details and all changes before May 2012 please see the (now discontinued) CHANGELOG in the source package (inst/ folder).

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

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.

sneumann/xcms documentation built on May 6, 2024, 11:23 a.m.

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sneumann/xcms LC-MS and GC-MS Data Analysis

NEWS.md In sneumann/xcms: LC-MS and GC-MS Data Analysis

xcms 4.1

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xcms 3.99

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xcms 3.21

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xcms 3.19

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xcms 3.17

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xcms 3.15

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xcms 3.13

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xcms 3.11

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xcms 3.9

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xcms 3.7

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xcms 3.5

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xcms 3.3

sneumann/xcms
LC-MS and GC-MS Data Analysis

NEWS.md
In sneumann/xcms: LC-MS and GC-MS Data Analysis