From 9fa4fa6a6dfc4efdfe001b5b7611fd23beb886c0 Mon Sep 17 00:00:00 2001 From: jorainer Date: Fri, 22 Mar 2024 09:51:31 +0100 Subject: [PATCH] Replace inst/NEWS with NEWS.md --- NEWS.md | 9 + inst/NEWS | 1560 ----------------------------------------------------- 2 files changed, 9 insertions(+), 1560 deletions(-) delete mode 100644 inst/NEWS diff --git a/NEWS.md b/NEWS.md index 6578300b6..47eefec67 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,14 @@ # xcms 4.1 +## 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. diff --git a/inst/NEWS b/inst/NEWS deleted file mode 100644 index 77bd2ba17..000000000 --- a/inst/NEWS +++ /dev/null @@ -1,1560 +0,0 @@ -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. - -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 3.99.6 ----------------------- - -- 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 3.21.5 ---------------------- - -- Fix issue in `chromatogram` after filtering a result object (issue #511). - -Changes in version 3.21.4 ---------------------- - -- Move multtest from Suggests to Imports in dependencies - -Changes in version 3.21.3 ---------------------- - -- Only fixes in the long running tests - -Changes in version 3.21.2 ---------------------- - -Changes in version 3.21.1 ---------------------- - -- Fix error with `fillChromPeaks` on sparse data (many empty spectra) and peak - detection performed with `MatchedFilterParam` (issue #653). -- Update to newer function names in the `rgl` package (issue #654). - -Changes in version 3.19.2 ----------------------- - -- Update/expand documentation for the `firstBaselineCheck` parameter of - centWave. - -Changes in version 3.19.1 ----------------------- - -- Update documentation to reference updates in MassSpecWavelet package. - -Changes in version 3.17.6 ----------------------- - -- Rewrite code to subset features and chromatographic peaks. This results in a - perfomance improvement for `filterFile` and similar functions. - -- Add parameter `expandMz` to `featureChromatograms` - (https://github.com/sneumann/xcms/issues/612). - -Changes in version 3.17.5 ----------------------- - -- Change the way the m/z value for a chromatographic peak is determined by - centWave: if a ROI contains more than one peak for one scan (spectrum) an - intensity-weighted m/z is reported for that scan. The m/z of the - chromatographic peak is then calculated based on these reported m/z values for - each scan (spectrum). In the original version the mean m/z for a scan was - reported instead. As a result, m/z values of chromatographic peaks are now - slightly different but are expected to be more accurate. See - https://github.com/sneumann/xcms/issues/590 for more details. - -Changes in version 3.17.4 ----------------------- - -- Add `transformIntensity` method. -- Fix issue when calling `chromPeakSpectra` or `featureSpectra` on an object - that contains also files with only MS1 spectra - (https://github.com/sneumann/xcms/issues/603). - -Changes in version 3.17.2 ----------------------- - -- Use mzML instead of mzData files in testing and vignettes, - since mzR drop mzData reading and msdata package will drop mzData files as well - -Changes in version 3.17.1 ----------------------- - -- Fix bug in feature grouping by EIC correlation that would return a - non-symmetric similarity matrix. -- Fix error message from issue [584](https://github.com/sneumann/xcms/issues/584). - -Changes in version 3.15.5 ----------------------- - -- Disable testing on windows i386, providing some speedup -- Disable parallel processing on Windows, causing an issue in testthat on BioC build check - -Changes in version 3.15.4 ----------------------- - -- Fix in `plot` with `type = "XIC"` to plot an empty plot if no data is present. -- Skip re-indexing of peaks to features if not necessary. This results in - performance improvements for MS1 only data. - -Changes in version 3.15.3 ----------------------- - -- Add `manualFeatures` allowing to manually define and add features to an - `XCMSnExp` object. -- Add `plotChromatogramsOverlay` function to support plotting of multiple EICs - from the same sample into the same plot (eventually stacked). -- Add feature grouping by EIC similarity: `EicSimilarityParam`. -- Import `compareChromatograms` from `MSnbase`. -- Add feature grouping by similar retention time: `SimilarRtimeParams. -- Add feature grouping by similarity of feature abundances across samples: - `AbundanceSimilarityParam`. -- Add feature grouping methodology based on `MsFeatures`. - -Changes in version 3.15.2 ----------------------- - -- Fix LC-MS/MS vignette. - -Changes in version 3.15.1 ----------------------- - -- Compatibility fix for nls() in R >= 4.1, contributed by Rick Helmus. - -Changes in version 3.13.8 ----------------------- - -- Fix plotQC() for XCMSnExp objects - -Changes in version 3.13.7 ----------------------- - -- Add `featureArea` function to extract the m/z-rt region for features. -- Fix `featureSpectra` function. -- Re-add the LC-MS/MS vignette. -- Feature: plotQC() supports XCMSnExp objects now - -Changes in version 3.13.6 ----------------------- - -- Fix issue #545: skip second centWave run with CentWavePredIsoParam in regions - of interest with undefined peak boundaries/scan ranges. -- Temporarily remove the LC-MS/MS vignette (until MsBackendMgf is added to - Bioconductor). - -Changes in version 3.13.5 ----------------------- - -- Add `filterChromPeaks` method to filter chromatographic peaks in a - `XChromatogram` or `XChromatograms` object. -- Add `filterChromPeaks` method for `XCMSnExp` (issue #541). -- Support return of `Spectra` objects by `chromPeakSpectra`, `featureSpectra` - and `reconstructChromPeakSpectra`. -- Support extraction of MS1 spectra with `chromPeakSpectra`. -- Support extraction of the spectrum with the largest total signal or largest - base peak signal in `chromPeakSpectra`. -- Add support for extraction of spectra for selected/individual peaks/features - using the `peaks` and `features` parameter in `chromPeakSpectra` and - `featureSpectra`, respectively. - -Changes in version 3.13.4 ----------------------- - -- Import `Param` object from `ProtGenerics`. -- Import `filterIntensity`, `normalize` and `alignRt` for `Chromatogram` and - `MChromatograms` from `MSnbase`. - - -Changes in version 3.13.3 ----------------------- - -- `align,Chromatogram` gains new method `"none"` which will only keep values - with identical retention times. For `method = "matchRtime"` the (much faster) - matching function `closest` from the `MsCoreUtils` package is used. -- Method `correlate,Chromatogram` gains parameter `useIntensitiesAbove` to - perform the correlation only with values larger than this threshold - (avoiding thus high correlation because of many 0-values). -- Add method `filterIntensity,Chromatogram` that allows to filter a chromatogram - object keeping only data points with an intensity above a user provided - threshold. - - -Changes in version 3.13.2 ----------------------- - -- Add new function `manualChromPeaks` allowing to manually add and integrate - chromatographic peaks. - - -Changes in version 3.13.1 ----------------------- - -- Support subsetting of `XChromatograms` with `drop = FALSE`. - - -Changes in version 3.11.8 ----------------------- - -- Disable parallel processing in vignettes. - - -Changes in version 3.11.7 ----------------------- - -- More efficient splitting data per file especially for larger data sets. -- Disable parallel processing in examples. - - -Changes in version 3.11.6 ----------------------- - -- Add `FilterIntensityParam` to filter chromatographic peaks on intensity - (issue #502). -- Add `estimatePrecursorIntensity` function to determine the precursor intensity - for MS2 spectra from the neighboring MS1 spectra. - - -Changes in version 3.11.4 ----------------------- - -- Change from `Spectra` and `Chromatograms` to `MSpectra` and `MChromatograms` - from MSnbase version >= 2.15.3. - - -Changes in version 3.11.3 ----------------------- - -- `reconstructChromPeakSpectra`: report also polarity and `precusorIntensity`. -- `reconstructChromPeakSpectra`: ensure a retention time is reported for - reconstructed MS2 spectra (issue #485). -- Change default for `expandRt` to `0` in `reconstructChromPeakSpectra`. -- Fix error in `refineChromPeaks,MergeNeighboringPeaksParam` if no peaks found - to be merged. - - -Changes in version 3.11.2 ----------------------- - -- Add `fillChromPeaks,ChromPeakAreaParam` to base the area from which missing - peak data should be filled-in on the actually detected chromatographic peaks - of a feature. -- Potential fix for issue #481: function should no longer throw an error because - retention times are of length 0. -- More efficient splitting of processing which should increase the speed of - the findChromPeaks, refineChromPeaks, reconstructChromPeakSpectra and - chromPeakSpectra calls. - - -Changes in version 3.11.1 ----------------------- - -- Fix issue #471: conversion from `XCMSnExp` to `xcmsSet` looses phenodata - (thanks to Andris Jankevics for reporting and providing a solution). -- Add `normalize` method for `Chromatogram` and `Chromatograms` objects. -- `featureChromatograms` gets new parameter `n` and `value` to extract EICs - only from the top n samples with highest intensities. -- `filterFile` gets new parameter `keepFeatures` to support retaining - correspondence results even if a data set is filtered by file. -- Export the virtual `Param` class. -- Add filterColumnsIntensityAbove method for Chromatograms object that allows - to select columns (samples) of an Chromatograms object for which intensities - of its chromatographic data are higher than a threshold. -- Add removeIntensity method for Chromatogram, Chromatograms, XChromatogram - and XChromatograms objects allowing to *remove* intensities based on different - criteria. -- Add correlate method for Chromatograms allowing to correlate multiple - chromatograms with each other. - - -Changes in version 3.9.4 ----------------------- - -- Fix issue in centWave which skips peak detection depending on minimum - peakwidth (issue #445): add parameter `extendLengthMSW` in `CentWaveParam`. - Thanks to William Kumler for contributing the fix. -- Tentatively reduce memory requirements in `fillChromPeaks`. -- Fix issue #467 for fillPeaks() of an xcmsSet converted from an XCMSnSet - -Changes in version 3.9.3 ----------------------- - -- Move multtest from Imports to Suggests to avoid duplicated method definition - for plot (issue #459). -- Add support for peak filling from MS level > 1 to fillChromPeaks. -- featureValues gains parameter msLevel to extract feature values for features - of all, or from a specific MS level. -- refineChromPeaks supports different MS levels. -- Added support to perform correspondence analysis on MS level > 1 and add the - respective results to already present feature definitions. -- hasChromPeaks and hasFeatures gain parameter msLevel to check for presence of - chromatographic peaks or features from a specific MS level. - - -Changes in version 3.9.2 ----------------------- - -- Fix featureChromatograms and chromatograms on a XCMSnExp object with features: - features can be duplicated across rows (EICs). -- findChromPeaks: add parameter `add` to allow several rounds of peak detections - on the same object. -- Small performance enhancement in fillChromPeaks. -- Better support for MS > 1 data in fillChromPeaks: skip MS level 2 spectra for - filling in. -- Add refineChromPeaks for XChromatogram and XChromatograms objects. -- Add groupOverlaps function to group arbitrary ranges. -- Add quantify,XCMSnExp object to quantify an XCMSnExp into a - SummarizedExperiment. -- Fine-tune MergeNeighboringPeaks peak refinement method: the average of the - 3 data points between candidate peaks is used to evaluate whether the peaks - should be merged making the approach more robust against outliers. In - addition, an ion chromatogram for candidate peaks is extracted with an m/z - range expanded depending on the expandMz and ppm setting ensuring that low - intensity data points between candidate peaks are not missed out (because - their m/z might be slightly shifted on ToF instruments). The mzmin and mzmax - of the merged peak represents also the minimum and maximum m/z of all data - points in that extracted ion chromatogram. - - -Changes in version 3.9.1 ----------------------- - -- Fix problem of not shown/plotted peak positions in plotChromPeakSpectra - for experiments in which peaks were not detected in the first sample(s). -- Add method *from_to* to missing value imputation method `imputeRowMinRand`. -- Show warning in findChromPeaks if empty spectra are detected. -- Add refineChromPeaks method and CleanPeaksParam class to allow removal of - chromatographic peaks exceeding a user-definable maximal peak width. -- Add MergeNeighboringPeaksParam for refineChromPeaks to allow merging of - chromatographic peaks close in m/z and retention time with a signal between - them higher than a certain threshold (issue #414). -- Fix misspelled parameter `mzd` in LC-MS/MS vignette. - - -Changes in version 3.7.5 ----------------------- - -- Remove xcmsMSn vignette (based on old xcms). - - -Changes in version 3.7.4 ----------------------- - -- mzClust correspondence analysis: check and fix missing values in column mz of - the peaks matrix (issue #416). - - -Changes in version 3.7.3 ----------------------- - -- plot type = "XIC" on an XCMSnExp object will draw rectangles indicating the - identified chromatographic peaks. -- Add a vignette describing LC-MS/MS data analysis with xcms. - - -Changes in version 3.7.2 ----------------------- - -- Fix documentation (issue #401). -- Add support for SWATH data analysis. - - -Changes in version 3.7.1 ----------------------- - -- Add correlate method for Chromatogram objects. -- Add parameter lwd to plotAdjustedRtime. -- Add align method for Chromatogram objects. -- Add findChromPeaksIsolationWindow to enable chromatographic peak detection - in isolation windows. -- Fix issue in chromPeakSpectra with method = "signal". -- chromPeakSpectra and featureSpectra return now MS2 spectra with an precursor - m/z >= mzmin, <= mzmax and retention time >= rtmin, <= rtmax. -- Improve performance of chromPeakSpectra and featureSpectra. - - -Changes in version 3.5.5 ----------------------- - -- Add dirname and dirname<- methods for OnDiskMSnExp to change the path to the - raw data files. -- Add section "Subset-based alignment" to the xcms vignette to describe the - alignment possibility to perform alignments based on a subset of samples - (e.g. QC samples). - - -Changes in version 3.5.4 ----------------------- - -- Fix problem in featureChromatograms with include = "feature_only" that could - return a non-valid object. -- Ensure that XCMSnExp objects are updated if necessary in all analysis methods. - - -Changes in version 3.5.3 ----------------------- - -- Fix unit tests. - - -Changes in version 3.5.2 ----------------------- - -- Small changes in fillChromPeaks,XCMSnExp to reduce memory demand. -- Fix issue #359. -- Fix issue #360: rawEIC skipped last scan/spectrum if rtrange was provided. -- filterMsLevel keeps now chromatographic peaks and feature definitions from the - specified MS levels (issue #362). -- Fix bug in `xcmsRaw` that leads to a netCDF error message (issue #363). -- Add parameter msLevel to chromPeaks for XCMSnExp objects. -- Add chromPeakData to allow adding arbitrary annotation to chromatographic - peaks. -- Change default of parameter value in featureValues from value = "index" to - value = "into". -- Add parameter isFilledColumn to chromPeaks allowing the old behaviour to - include the is_filled column in the chromatographic peak matrix. - - -Changes in version 3.5.1 ----------------------- - -- Fix issue #349. -- Add updateObject function for XCMSnExp objects (issue #347). -- Add dropFilledChromPeaks methods for XChromatogram and XChromatograms objects. -- Add parameter filled = FALSE to chromatogram and featureChromatograms - functions. -- Fix matchedFilter peak detection problems with empty spectra (issue #325). -- featureChromatograms extracts by default only chromatographic peaks associated - with a feature. -- chromatogram,XCMSnExp extracts an XChromatogram containing also - chromatographic peaks and feature definitions. -- Add featureValues method for XChromatograms objects (issue #336). -- Add correspondence analysis (peak grouping) for chromatographic data (for now - only with PeakDensity method; issue #336). -- Add featureDefinitions slot to XChromatograms object and related accessor - methods. -- Add subset alignment option subsetAdjust = "average" to adjust left-out - samples (blanks or simply non-subset samples) based on an interpolation from - the results of the previous and subsequent subset sample. -- Add parameter subsetAdjust to PeakGroupsParam allowing to switch between - different methods to adjust samples left out in the alignment process. -- Alignment based on a sample subset for the peak groups method (issue #335): - sample subset can be defined with the subset parameter, samples not included - in the subset will be aligned based on the adjusted retention times of the - closest sample in the subset. -- Add findChromPeaks,XChromatograms (issue #332). -- Add processHistory,XChromatograms. -- Add plot,XChromatograms method with automatic peak highlighting (issue #334). -- Add hasChromPeaks,XChromatograms method. -- Add XChromatograms class with constructor function and coercing method. -- Add hasChromPeaks,XChromatogram method. -- Add filterRt,XChromatogram, filterMz,XChromatogram. -- Add plot,XChromatogram function supporting of highlighting/drawing identified - chromatographic peaks. -- findChromPeaks,Chromatogram returns an XChromatogram object (issue #329). -- Add chromPeaks,XChromatogram (issue #329). -- Add XChromatogram object (issue #329). -- Fix higlightChromPeaks with type = "polygon": peak filling represents now the - full detected peak and is no longer cut by the provided rt. -- Add argument peakIds to highlightChromPeaks allowing to specify the IDs of - peaks to be highlighted. -- Add example on clustering of base peak chromatograms to the vignette (issue - #328). -- Small fix in the vignette (issue #327). -- Add parameter groupval to exportMetaboAnalyst (issue #296). -- Fix bug in show,XCMSnExp that would throw an error if no process history is - present. - - -Changes in version 3.3.6 ----------------------- - -- Add type = "polygon" to highlightChromPeaks allowing to fill the actual - signal area of identified chromatographic peaks. - - -Changes in version 3.3.5 ----------------------- - -- Performance enhancement of the chromPeakSpectra and featureSpectra functions. - - -Changes in version 3.3.4 ----------------------- - -- Add featureChromatograms to extract ion chromatograms for each feature. -- Add hasFilledChromPeaks function. -- Add argument skipFilled to the featureSummary function. - - -Changes in version 3.3.3 ----------------------- - -- Add chromPeakSpectra and featureSpectra functions to extract MS2 spectra - for chromatographic peaks and features, respectively (issue #321). -- Fix profMat to handle also data files with empty spectra (issue #312). -- Add argument ylim to plotAdjustedRtime (issue #314). -- Add imputeRowMin and imputeRowMinRand, two simple missing value imputation - helper functions. -- Fix additional problem mentioned in issue #301 with obiwarp retention time - correction if some spectra have m/z values of `NA`. -- Fix issue #300 avoiding chromatographic peaks with rtmin > rtmax. -- Fixes for issues #291, #296. -- Add parameter 'missing' to diffreport allowing to replace NA with arbitrary - numbers. -- Add exportMetaboAnalyst function to export the feature matrix in MetaboAnalyst - format. -- Add parameter missing to featureValues allowing to specify how to handle/ - report missing values. -- The chromPeaks matrix has now rownames to uniquely identify chromatographic - peaks in an experiment. Chromatographic peak IDs start with "CP" followed by - a number. - - -Changes in version 3.3.2 ----------------------- - -- Add writeMSData method for XCMSnExp allowing to write mzML/mzXML files with - adjusted retention times (issue #294). -- Fix profEIC call for single-scan-peak (pull request #287 from @trljcl). -- Fix centWave avoiding that the same peak is reported multiple times if - fitgauss = TRUE is used (issue #284). -- featureSummary reports also RSD (relative standard deviations) of features - across samples (issue #286). -- Add parameters fixedMz and fixedRt to FillChromPeaksParam that allow to - increase the features' m/z and rt widths by a constant factor. -- Add option "sum" to featureValues' method parameter allowing to sum the - intensities of peaks that are assigned to the same feature in a file/sample. - - -Changes in version 3.3.1 ----------------------- - -- Add overlappingFeatures function to identify overlapping or close features. -- Add support for type = "apex_within" for featureDefinitions. -- Fix a bug in fillChromPeaks that would return the integrated signal being Inf. -- Fix for issue #267: error in fillChromPeaks when the retention time of the - peaks are outside of the retention time range of certain files. -- New featureSummary function to calculate basic feature summaries (number of - samples in which peaks were found etc). -- Parameter 'type' added to plotChromPeakDensity and 'whichPeaks' to - highlightChromPeaks. Both parameters are passed to the 'type' argument - of chromPeaks. -- Parameter 'type' in chromPeaks gets additional option "apex_within" to return - chromatographic peaks that have their apex within the defined rt and/or m/z - range. -- Add functions rla and rowRla to calculate RLA (relative log abundances). -- Add peaksWithMatchedFilter to perform peak detection in chromatographic - (MRM/SRM) data (issues #277 and #278). -- Add peaksWithCentWave to perform centWave peak detection in chromatographic - (MRM/SRM) data (issue #279). -- Add findChromPeaks,Chromatogram methods for CentWaveParam and - MatchedFilterParam (issue #280). - - -Changes in version 3.1.3 ----------------------- - -BUG FIXES: -- Fix misplaced parenthesis in the check for multiple spectra in - findChromPeaks,OnDiskMSnExp,MSWParam. Thanks to @RonanDaly (PR #276). -- Update link to correct metlin page in diffreport result (issue #204). - - -Changes in version 3.1.2 ----------------------- - -NEW FEATURES -- Add filterFeatureDefinitions function. - -BUG FIXES: -- Fix #273: better error message in case not a single feature could be defined - by groupChromPeaks. - - -Changes in version 3.1.1 ----------------------- - -NEW FEATURES -- Reading raw files using xcmsSet or xcmsRaw uses now the automatic file type - detection feature from mzR. -- c function to concatenate XCMSnExp objects. -- groupnames method for XCMSnExp objects (issue #250). - -BUG FIXES: -- Fix #237: findPeaks.MSW was not throwing an error if applied to multi-spectrum - MS file. -- Fix #249: quantile call in adjustRtime PeakGroups without na.rm = TRUE. -- Fix #259 - - -Changes in version 2.99.10 ----------------------- - -BUG FIXES: -- Fix #230: Failing vignettes on Windows. - - -Changes in version 2.99.9 ----------------------- - -USER VISIBLE CHANGES: -- Chromatographic peak detection uses adjusted retention times on an aligned - XCMSnExp object (issue #213, #208). -- New parameter msLevel for processHistory,XCMSnExp. -- New parameter keepAdjustedRtime for filterMsLevel,XCMSnExp, dropChromPeaks, - XCMSnExp and dropFeatureDefinitions,XCMSnExp. -- Add parameter msLevel to chromatogram,XCMSnExp method (issue #205). -- Obiwarp alignment is now performed on one MS level and adjustment is applied - to all MS levels (issue #214). -- Add function plotMsData to plot intensity against retention time and m/z - against retention time for a MS slice in one sample. -- Add argument msLevel = 1L to extractMsData method (issue #223). -- New applyAdjustedRtime function to consolidate the alignment results, i.e. - replace the raw retention times in the XCMSnExp with the adjusted retention - times. -- [,XCMSnExp method gains argument keepAdjustedRtime to allow keeping adjusted - retention times in the sub-setting. -- Implement spectrapply,XCMSnExp to ensure returned results use adjusted - retention times (if present). -- [[,XCMSnExp method returns a Spectrum object with adjusted retention time, if - the XCMSnExp contains adjusted retention times. -- Argument 'sampleGroups' is mandatory for 'PeakDensityParam' (issue #228). - -BUG FIXES: -- Fix #191: Excessive memory use in fillPeaks. -- Fix #220: peaks matrix is missing column "sample" if no peaks were found in - the first sample. -- Fix #222: findChromPeaks does not return an XCMSnExp object filtered to a - single MS level despite peak detection is performed on a single level. -- Fix problem in plotMsData causing wrong colors to be used to label the data - points. - - -Changes in version 2.99.8 ----------------------- - -BUG FIXES: -- Replace xcmsMSn Rnw with Rmd vignette to fix Windows build errors. - - -Changes in version 2.99.7 ----------------------- - -BUG FIXES: -- Fix #201: Warnings: 'readMSData2' is deprecated, thanks to L. Gatto. -- Merge with BioC git after transition - - -Changes in version 2.99.6 ----------------------- - -NEW FEATURES: -- calibrate,XCMSnExp method that allows to calibrate chromatographic peaks. - -USER VISIBLE CHANGES: -- Export phenoDataFromPaths function (issue $195). -- Add arguments mz and rt to featureDefinitions method allowing to extract - features within the specified ranges. -- Increase n for the density function call in group density-based correspondence - by 2. -- Replace xcmsDirect.Rnw with rmarkdown-based vignette using the new user - interface. - -BUG FIXES: -- issue #196: removed the unnecessary requirement for same-dimension profile - matrices in adjustRtime,XCMSnExp,ObiwarpParam. -- issue #194: fixes in retcor.obiwarp: 1) subset raw data if scanrange != NULL. - 2) if the mz range of the two files to be aligned differ, expand them - correctly. Depending on the profStep and the mz values/ranges the matrices - were not expanded correctly. -- Potential problems in the plotChromPeakDensity function. - - -Changes in version 2.99.5 ----------------------- - -USER VISIBLE CHANGES: -- Re-enable sleep parameter in findPeaks.centWave and findPeaks.matchedFilter. - - -Changes in version 2.99.4 ----------------------- - -NEW FEATURES: -- Add plotChromPeaks function to plot the definition (rt and mz range) of - detected chromatographic peaks of one file into the mz-rt plane. -- Add plotChromPeakImage function to plot the number of detected peaks along - the retention time axis per file as an image plot. - -USER VISIBLE CHANGES: -- Move Chromatogram class and functionality to the MSnbase package -- Add argument msLevel to the findChromPeaks method to allow (chromatographic) - peak detection also on MS level > 1. - -BUG FIXES: -- Polarity information was not read from mzXML files (issue #192). - - -Changes in version 2.99.3 ----------------------- - -BUG FIXES: -- issue #188: determine file type from file content if file ending not known. - - -Changes in version 2.99.2 ----------------------- - -BUG FIXES: -- issue #181: problem when isCentroided,Spectrum method returns NA because of - too few peaks in a spectrum. Fixed by checking in such cases all spectra in - the file. -- issue #184: add parameter sleep to do_groupChromPeaks_density function to be - backwards compatible with the old group.density code. - - -Changes in version 2.99.1 ----------------------- - -NEW FEATURES: -- extractMsData to extract raw MS data as a data.frame (issue #120). - -BUG FIXES: -- issue #175: an error is now thrown if no peak group was identified for peak - group retention time correction. -- issue #178: scanrange was collapsed when the adjusted range was reported - (pull request by Jan Stanstrup). -- issue #180: error when both parameters method and smooth are provided in the - retcor method. - - -Changes in version 2.99.0 ----------------------- - -NEW FEATURES: -- plotChromatogram and highlightChromPeaks functions. -- plotChromPeakDensity function. -- clean method for Chromatogram classes. - -USER VISIBLE CHANGES: -- Change default for ppm parameter in chromPeaks method to 0. -- extractChromatograms supports extraction of multiple rt and mz ranges. -- New parameter missing for extractChromatograms allowing to specify the - intensity value to be used for rts for which no signal is available within - the mz range. -- extractChromatograms returns Chromatograms of length equal to the number of - scans within the specified rt range, even if no signals are measured - (intensity values are NA). - - -Changes in version 1.53.1 ----------------------- - -BUG FIXES: -- Increase parameter n for the density call in the peak density correspondence - method. This enables to separate neighboring peaks using small n (issue #161). - Thanks to Jan Stanstrup. - - -Changes in version 1.51.11 ----------------------- - -NEW FEATURES: -- Parameter "filled" for featureValues (issue #157). -- Parameters "rt" and "mz" in chromPeaks method allowing to extract - chromatographic peaks from the specified ranges (issue #156). - -BUG FIXES: -- Fixed possible memory problem in obiwarp (issue #159). -- Update getPeaks to use non-deprecated API (issue #163). - - -Changes in version 1.51.10 ----------------------- - -NEW FEATURES: -- filterRt for Chromatogram class (issue #142). -- adjustRtimePeakGroups function (issue #147). -- adjustRtime,XCMSnExp,PeakGroupsParam and do_adjustRtime_peakGroups support - use of pre-defined matrix to perform alignment (issue #153). -- plotAdjustedRtime to visualize alignment results (issue #141). - -USER VISIBLE CHANGES: -- featureDefinitions and featureValues return DataFrame and matrix with rownames - corresponding to arbitrary feature IDs (issue #148). -- New peakGroupsMatrix slot for PeakGroupsParam class (issue #153). - -BUG FIXES: -- Issue #146: ensure adjusted retention times returned by the peakGroups method - to be in the same order than the raw retention times. - - -Changes in version 1.51.9 ----------------------- - -NEW FEATURES: -- fillChromPeaks, dropFilledChromPeaks methods and FillChromPeaksParam class. -- featureValues method. - -USER VISIBLE CHANGES: -- Extended new_functionality vignette. -- Change default backend for reading mzML files to pwiz. - -BUG FIXES: -- Issue #135: fix peak signal integration for centWave. -- Issue #139: problem with expand.mz and expand.rt in fillPeaks.chrom. -- Issue #137: Error in findChromPeaks if no peaks are found. - - -Changes in version 1.51.8 ----------------------- - -NEW FEATURES: -- Add Chromatogram class and extractChromatograms method. - -BUG FIXES: -- Issue #118: failing unit test on Windows build machine. -- Issue #133: error with c() and xcmsSet without peaks. -- Issue #134: xcmsSet constructor endless loop. - - -Changes in version 1.51.7 ----------------------- - -USER VISIBLE CHANGES: -- Major renaming of methods and classes to follow the naming convention: - - chromatographic peak (chromPeak): the peaks identified in rt dimension. - - feature: mz-rt feature, being the grouped chromatographic peaks within and - across samples. - -BUG FIXES: -- Issue #127: failing unit test on Windows build machine. - - -Changes in version 1.51.6 ----------------------- - -NEW FEATURES: -- groupFeatures and adjustRtime methods for XCMSnExp objects. -- New Param classes for groupFeatures and adjustRtime analysis methods: FeatureDensityParam, - MzClustParam, NearestFeaturesParam, FeatureGroupsParam and ObiwarpParam. - -BUG FIXES: -- Issue #124 (filterRt,XCMSnExp returned empty object). - - -Changes in version 1.51.5 ----------------------- - -NEW FEATURES: -- MsFeatureData and XCMSnExp objects. -- features, features<-, adjustedRtime, adjustedRtime<-, featureGroups, - featureGroups<-, hasAlignedFeatures, hasAdjustedRtime and hasDetectedFeatures - methods. -- dropFeatures, dropFeatureGroups and dropAdjustedRtime methods. -- filterMz, filterRt, filterFile etc implemented. -- mz, intensity and rtime methods for XCMSnExp allowing to return values grouped - by sample. - -BUG FIXES: -- Issue #99 (rtrange outside of retention time range in getEIC,xcmsSet). -- Issue #101 (xcmsRaw function returns NULL if mslevel = 1 is specified). -- Issue #102 (centWave returns empty matrix if scales not OK). Thanks to J. Stanstrup. -- Issue #91 (warning instead of error if no peaks in ROI). Thanks to J. Stanstrup. - - -Changes in version 1.51.4 ----------------------- - -BUG FIXES: -- added deepCopy to avoid corrupting the original object, thanks to J. Stanstrup, closes #93 - - -Changes in version 1.51.3 ----------------------- - -NEW FEATURES: -- binYonX binning function. -- imputeLinInterpol function providing linear interpolation of missing values. -- breaks_on_binSize and breaks_on_nBins functions to calculate breaks defining - bins. -- New vignette "new_functionality.Rmd" describing new and modified functionality - in xcms. -- Add do_detectFeatures_matchedFilter function. -- Add do_detectFeatures_centWave function. -- Add do_detectFeatures_centWaveWithPredIsoROIs function and unit test. -- Implement a new data import function. -- Add do_detectFeatures_MSW function and unit test. -- Argument stopOnError in xcmsSet function that allows to perform feature - detection on all files without stopping on errors. -- Method showError for xcmsSet objects that list all errors during feature - detection (if stopOnError = FALSE in the xcmsSet function). -- [ method to subset xcmsRaw objects by scans. -- profMat method to extract/create the profile matrix from/for an xcmsRaw. -- Add new detectFeatures methods for MSnExp and OnDiskMSnExp objects from the - MSnbase package. -- Add new CentWaveParam, MatchedFilterParam, MassifquantParam, MSWParam and - CentWavePredIsoParam parameter class to perform method dispatch in the - detectFeatures method. -- retcor.obiwarp uses the new binning methods for profile matrix generation. -- scanrange,xcmsRaw reports always a scanrange of 1 and length(object@scantime). -- scanrange,xcmsSet reports the scanrange eventually specified by the user in - the xcmsSet function. -- Fixed bug in rawMat (issue #58). -- Fix issue #60: findPeaks.massifquant always returns a xcmsPeaks object. - - -Changes in version 1.51.2 ----------------------- - -USER VISIBLE CHANGES: -- As suggested by Jan Stanstrup, do not error if a centWave ROI - contains no data, closes #90 - -Changes in version 1.51.1 ----------------------- - -BUG FIXES: -- Fix incorrrect indexing getEIC function reported by Will Edmands, closes #92 - - -Changes in version 1.49.7 ----------------------- - -BUG FIXES: -- Fix documentation warnings. - - -Changes in version 1.49.6 ----------------------- - -USER VISIBLE CHANGES: -- Peak Picking function findPeaks.centWaveWithPredictedIsotopeROIs() and findPeaks.addPredictedIsotopeFeatures(), - which allow more sensitive detection of isotope features. - - -Changes in version 1.49.5 ----------------------- - -USER VISIBLE CHANGES: -- Some documentation updates. -- Preparation for a new binning function - - -Changes in version 1.49.4 ----------------------- - -BUG FIXES: -- Fix getXcmsRaw that would prevent retention time correction to be applied - (issue #44 reported by Aleksandr). - - -Changes in version 1.49.3 ----------------------- - -NEW FEATURE: -- updateObject method for xcmsSet. - -USER VISIBLE CHANGES: -- xcms uses now BiocParallel for parallel processing. All other parallel - processing functions have been deprecated. - -BUG FIXES: -- 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. - -OTHER CHANGES -- 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 ----------------------- - -NEW FEATURE: - -- 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 ----------------------- - -NEW FEATURE: - -- 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 1.47.3 ----------------------- - -- Disable parallel processing in unit tests causing a timeout - on BioC build machines - - -Changes in version 1.47.2 ----------------------- - -BUG FIXES -- 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 ----------------------- - -USER VISIBLE CHANGES: -- Disabled parallel processing in unit tests -* migrate dependencies from ncdf -> ncdf4 - - -Changes in version 1.45.7 ----------------------- - -USER VISIBLE CHANGES: -- Disabled Rmpi support and usage on Windows - - -Changes in version 1.45.6 ----------------------- - -NEW FEATURE: -- J. Rainer implemented a [ method that allows to subset an xcmsSet. - -BUG FIXES: -- 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 ----------------------- - -USER VISIBLE CHANGES: -- 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. - -BUG FIXES: -- 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 ----------------------- - -BUG FIXES: -- Fixed a bug in the levelplot method for xcmsSet. - - -Changes in version 1.45.3 ----------------------- - -NEW FEATURE: - -- 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. - -USER VISIBLE CHANGES: -- 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). - -BUG FIXES: -- 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 ----------------------- - -BUG FIXES: - o 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 ----------------------- - -NEW FEATURE: - o plotrt now allows col to be a vector of color definition, - same as the plots for retcor methods. - o Added $ method to access phenoData columns in a eSet/ExpressionSet like manner. - o Allow to use the "parallel" package for parallel processing of the functions xcmsSet and fillPeaks.chrom. - o Thanks to J. Rainer! - - -Changes in version 1.43.3 ----------------------- - -BUG FIXES: - o Give a more verbose error message when file not found - - -Changes in version 1.43.2 ----------------------- - -BUG FIXES: - o Use ProtGenerics, adapted xcms peaks() - - -Changes in version 1.43.1 ----------------------- - -NEW FEATURE: - o function plotQC() for plotting various QC plots on RT and m/z - - -Changes in version 1.41.1 ----------------------- - -BUG FIXES: - o fix sampclass generation from phenoData if some combinations of factors don't exist - o disable parallel code in manpages to avoid issues on BioC windows build farm machines - - -Changes in version 1.39.6 ----------------------- - -USER VISIBLE CHANGES: - o Massifquant reports the maximum intensity for each isotope trace -(peak). This is useful for interactive parameter optimization. -BUG FIXES: - o 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 ----------------------- - -BUG FIXES: - o Fixed write.cdf(), which had an intensity offset of +1, added a unit test - - -Changes in version 1.39.3 ----------------------- - -BUG FIXES: - o 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 ----------------------- - -BUG FIXES: - o Updated doubleMatrix c code to allow for larger profile matrixes - -REQUIRED CHANGES - o Moved inst/doc to vignettes - - -Changes in version 1.37.6 ----------------------- - -NEW FEATURE: - o Introducing write.mzQuantML(xcmsSet) to export the peak list and grouped matrix to the PSI format mzQuantML (see http://www.psidev.info/mzquantml) -USER VISIBLE CHANGES: - o Add Brigham Young University to LICENSE file for copyright purposes. - o Add copyright information display when running findPeaks.massifquant() - within xcmsRaw.R - o Clean and update documentation for findPeaks.massifquant-methods.Rd -BUG FIXES: - o Remove unused parameters in findKalmanROIs() within xcmsRaw.R - - -Changes in version 1.37.5 ----------------------- - -BUG FIXES - o 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 ----------------------- - -BUG FIXES - o Skip t-test in diffreport() if one class has less than 2 samples. - - -Changes in version 1.37.3 ----------------------- - -BUG FIXES - o 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 ----------------------- - -BUG FIXES - o 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 ----------------------- - -NEW FEATURES: - o Introducing msn2xcmsRaw, to allow findPeaks() on MS2 and MSn data - - -Changes in version 1.35.7 ----------------------- - -BUG FIXES - o 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 ----------------------- - -BUG FIXES - o 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 ----------------------- - -NEW FEATURES: - o Introducing parallel fillPeaks - -USER VISIBLE CHANGES - o Replace snow requirement with minimum R version 2.14.0 - - -Changes in version 1.35.3 ----------------------- - -BUG FIXES - o 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 ----------------------- - -UPDATED FEATURES: - o 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 -BUG FIXES - o massifquant: simplified logic structure of Tracker::claimDataIdx - resolved failure on new test case. - o massifquant: reporting features data structure compatible with - multiple sample comparison within XCMS. - - -Changes in version 1.35.1 ----------------------- - -UPDATED FEATURES: - o The mzData export is now much faster and uses less memory - - -Changes in version 1.33.16 ----------------------- - -USER VISIBLE CHANGES - - o 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 ----------------------- - -UPDATED FEATURES: - o 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 ----------------------- - -BUG FIXES - - o scanrage is now honoured in xcmsSet, also when in parallel mode - - -Changes in version 1.33.14 ----------------------- - -BUG FIXES - - o scanrage is now honoured in xcmsRaw, and consequently - also in xcmsSet(matchedFilter), where previously - it was ignored. - - -Changes in version 1.33.13 ----------------------- - -BUG FIXES - - o write.cdf() has been fixed to write files AMDIS can read - - -Changes in version 1.33.12 ----------------------- - -BUG FIXES - - o write.mzData adds Polarity to the file if available - - -Changes in version 1.33.11 ----------------------- - -USER VISIBLE CHANGES - - o centWave uses a new method to estimate local noise which improves detection of closely spaced peaks - -NEW FEATURES - - o placeholder - -BUG FIXES - - o group.mzClust was failing when result had one peak - - -+ 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.