XCMSnExp-class {xcms} | R Documentation

## Data container storing xcms preprocessing results

### Description

The `XCMSnExp` object is designed to contain all results from metabolomics data preprocessing (chromatographic peak detection, peak grouping (correspondence) and retention time correction). The corresponding elements in the `msFeatureData` slot are `"chromPeaks"` (a `matrix`), `"featureDefinitions"` (a `DataFrame`) and `"adjustedRtime"` (a `list` of numeric vectors). Note that these should not be accessed directly but rather via their accessor methods.

Along with the results, the object contains the processing history that allows to track each processing step along with the used settings. This can be extracted with the `processHistory` method.

The `XCMSnExp` object directly extends the `OnDiskMSnExp` object and provides thus an easy access to the full raw data at any stage of an analysis.

Objects from this class should not be created directly, they are returned as result from the `findChromPeaks` method.

`XCMSnExp` objects can be coerced into `xcmsSet` objects using the `as` method.

`processHistoryTypes` returns the available types of process histories. These can be passed with argument `type` to the `processHistory` method to extract specific process step(s).

`profMat`: creates a profile matrix, which is a n x m matrix, n (rows) representing equally spaced m/z values (bins) and m (columns) the retention time of the corresponding scans. Each cell contains the maximum intensity measured for the specific scan and m/z values. See `profMat` for more details and description of the various binning methods.

`hasAdjustedRtime`: whether the object provides adjusted retention times.

`hasFeatures`: whether the object contains correspondence results (i.e. features).

`hasChromPeaks`: whether the object contains peak detection results.

`adjustedRtime`,`adjustedRtime<-`: extract/set adjusted retention times. `adjustedRtime<-` should not be called manually, it is called internally by the `adjustRtime` methods. For `XCMSnExp` objects, `adjustedRtime<-` does also apply retention time adjustments to eventually present chromatographic peaks. The `bySample` parameter allows to specify whether the adjusted retention time should be grouped by sample (file).

`featureDefinitions`, `featureDefinitions<-`: extract or set the correspondence results, i.e. the mz-rt features (peak groups). Similar to the `chromPeaks` it is possible to extract features for specified m/z and/or rt ranges (see `chromPeaks` for more details).

`chromPeaks`, `chromPeaks<-`: extract or set the matrix containing the information on identified chromatographic peaks. Parameter `bySample` allows to specify whether peaks should be returned ungrouped (default `bySample = FALSE`) or grouped by sample (`bySample = TRUE`). The `chromPeaks<-` method for `XCMSnExp` objects removes also all correspondence (peak grouping) and retention time correction (alignment) results. The optional arguments `rt`, `mz` and `ppm` allow to extract only chromatographic peaks overlapping (if `type = "any"`) or completely within (if `type = "within"`) the defined retention time and mz ranges. See description of the return value for details on the returned matrix. Users usually don't have to use the `chromPeaks<-` method directly as detected chromatographic peaks are added to the object by the `findChromPeaks` method.

`rtime`: extracts the retention time for each scan. The `bySample` parameter allows to return the values grouped by sample/file and `adjusted` whether adjusted or raw retention times should be returned. By default the method returns adjusted retention times, if they are available (i.e. if retention times were adjusted using the `adjustRtime` method).

`mz`: extracts the mz values from each scan of all files within an `XCMSnExp` object. These values are extracted from the original data files and eventual processing steps are applied on the fly. Using the `bySample` parameter it is possible to switch from the default grouping of mz values by spectrum/scan to a grouping by sample/file.

`intensity`: extracts the intensity values from each scan of all files within an `XCMSnExp` object. These values are extracted from the original data files and eventual processing steps are applied on the fly. Using the `bySample` parameter it is possible to switch from the default grouping of intensity values by spectrum/scan to a grouping by sample/file.

`spectra`: extracts the `Spectrum` objects containing all data from `object`. The values are extracted from the original data files and eventual processing steps are applied on the fly. By setting `bySample = TRUE`, the spectra are returned grouped by sample/file. If the `XCMSnExp` object contains adjusted retention times, these are returned by default in the `Spectrum` objects (can be overwritten by setting `adjusted = FALSE`).

`processHistory`: returns a `list` with `ProcessHistory` objects (or objects inheriting from this base class) representing the individual processing steps that have been performed, eventually along with their settings (`Param` parameter class). Optional arguments `fileIndex`, `type` and `msLevel` allow to restrict to process steps of a certain type or performed on a certain file or MS level.

`dropChromPeaks`: drops any identified chromatographic peaks and returns the object without that information. Note that for `XCMSnExp` objects the method drops by default also results from a correspondence (peak grouping) analysis. Adjusted retention times are removed if the alignment has been performed after peak detection. This can be overruled with `keepAdjustedRtime = TRUE`.

`dropFeatureDefinitions`: drops the results from a correspondence (peak grouping) analysis, i.e. the definition of the mz-rt features and returns the object without that information. Note that for `XCMSnExp` objects the method will also by default drop retention time adjustment results, if these were performed after the last peak grouping (i.e. which base on the results from the peak grouping that are going to be removed). All related process history steps are removed too as well as eventually filled in peaks (by `fillChromPeaks`). The parameter `keepAdjustedRtime` can be used to avoid removal of adjusted retention times.

`dropAdjustedRtime`: drops any retention time adjustment information and returns the object without adjusted retention time. For `XCMSnExp` objects, this also reverts the retention times reported for the chromatographic peaks in the peak matrix to the original, raw, ones (after chromatographic peak detection). Note that for `XCMSnExp` objects the method drops also all peak grouping results if these were performed after the retention time adjustment. All related process history steps are removed too.

`findChromPeaks` performs chromatographic peak detection on the provided `XCMSnExp` objects. For more details see the method for `XCMSnExp`. Note that the `findChromPeaks` method for `XCMSnExp` objects removes previously identified chromatographic peaks and aligned features. Previous alignment (retention time adjustment) results are kept, i.e. chromatographic peak detection is performed using adjusted retention times if the data was first aligned using e.g. obiwarp (`adjustRtime-obiwarp`).

`dropFilledChromPeaks`: drops any filled-in chromatographic peaks (filled in by the `fillChromPeaks` method) and all related process history steps.

description `spectrapply` applies the provided function to each `Spectrum` in the object and returns its results. If no function is specified the function simply returns the `list` of `Spectrum` objects.

### Usage

    processHistoryTypes()

    ## S4 method for signature 'OnDiskMSnExp'
    profMat(object, method = "bin", step = 0.1,
      baselevel = NULL, basespace = NULL, mzrange. = NULL, fileIndex, ...)

    ## S4 method for signature 'XCMSnExp'
    show(object)

    ## S4 method for signature 'XCMSnExp'
    hasAdjustedRtime(object)

    ## S4 method for signature 'XCMSnExp'
    hasFeatures(object)

    ## S4 method for signature 'XCMSnExp'
    hasChromPeaks(object)

    ## S4 method for signature 'XCMSnExp'
    adjustedRtime(object, bySample = FALSE)

    ## S4 replacement method for signature 'XCMSnExp'
    adjustedRtime(object) <- value

    ## S4 method for signature 'XCMSnExp'
    featureDefinitions(object, mz = numeric(),
      rt = numeric(), ppm = 0, type = "any")

    ## S4 replacement method for signature 'XCMSnExp'
    featureDefinitions(object) <- value

    ## S4 method for signature 'XCMSnExp'
    chromPeaks(object, bySample = FALSE, rt = numeric(),
      mz = numeric(), ppm = 0, type = "any")

    ## S4 replacement method for signature 'XCMSnExp'
    chromPeaks(object) <- value

    ## S4 method for signature 'XCMSnExp'
    rtime(object, bySample = FALSE,
      adjusted = hasAdjustedRtime(object))

    ## S4 method for signature 'XCMSnExp'
    mz(object, bySample = FALSE, BPPARAM = bpparam())

    ## S4 method for signature 'XCMSnExp'
    intensity(object, bySample = FALSE,
      BPPARAM = bpparam())

    ## S4 method for signature 'XCMSnExp'
    spectra(object, bySample = FALSE,
      adjusted = hasAdjustedRtime(object), BPPARAM = bpparam())

    ## S4 method for signature 'XCMSnExp'
    processHistory(object, fileIndex, type, msLevel)

    ## S4 method for signature 'XCMSnExp'
    dropChromPeaks(object, keepAdjustedRtime = FALSE)

    ## S4 method for signature 'XCMSnExp'
    dropFeatureDefinitions(object, keepAdjustedRtime = FALSE,
      dropLastN = -1)

    ## S4 method for signature 'XCMSnExp'
    dropAdjustedRtime(object)

    ## S4 method for signature 'XCMSnExp'
    profMat(object, method = "bin", step = 0.1,
      baselevel = NULL, basespace = NULL, mzrange. = NULL, fileIndex, ...)

    ## S4 method for signature 'XCMSnExp,Param'
    findChromPeaks(object, param, BPPARAM = bpparam(),
      return.type = "XCMSnExp", msLevel = 1L)

    ## S4 method for signature 'XCMSnExp'
    dropFilledChromPeaks(object)

    ## S4 method for signature 'XCMSnExp'
    spectrapply(object, FUN = NULL, BPPARAM = bpparam(),
      ...)

### Arguments

`object` | For `adjustedRtime`, `featureDefinitions`, `chromPeaks`, `hasAdjustedRtime`, `hasFeatures` and `hasChromPeaks` either a `MsFeatureData` or a `XCMSnExp` object, for all other methods a `XCMSnExp` object.
`method` | The profile matrix generation method. Allowed are `"bin"`, `"binlin"`, `"binlinbase"` and `"intlin"`. See details section for more information.
`step` | numeric(1) representing the m/z bin size.
`baselevel` | numeric(1) representing the base value to which empty elements (i.e. m/z bins without a measured intensity) should be set. Only considered if `method = "binlinbase"`. See `baseValue` parameter of `imputeLinInterpol` for more details.
`basespace` | numeric(1) representing the m/z length after which the signal will drop to the base level. Linear interpolation will be used between consecutive data points falling within `2 * basespace` to each other. Only considered if `method = "binlinbase"`. If not specified, it defaults to `0.075`. Internally this parameter is translated into the `distance` parameter of the `imputeLinInterpol` function by `distance = floor(basespace / step)`. See `distance` parameter of `imputeLinInterpol` for more details.
`mzrange.` | Optional numeric(2) manually specifying the mz value range to be used for binnind. If not provided, the whole mz value range is used.
`fileIndex` | For `processHistory`: optional `numeric` specifying the index of the files/samples for which the `ProcessHistory` objects should be retrieved.
`...` | Additional parameters.
`bySample` | logical(1) specifying whether results should be grouped by sample.
`value` | For `adjustedRtime<-`: a `list` (length equal to the number of samples) with numeric vectors representing the adjusted retention times per scan. For `featureDefinitions<-`: a `DataFrame` with peak grouping information. See return value for the `featureDefinitions` method for the expected format. For `chromPeaks<-`: a `matrix` with information on detected peaks. See return value for the `chromPeaks` method for the expected format.
`mz` | optional `numeric(2)` defining the mz range for which chromatographic peaks should be returned.
`rt` | optional `numeric(2)` defining the retention time range for which chromatographic peaks should be returned.
`ppm` | optional `numeric(1)` specifying the ppm by which the `mz` range should be extended. For a value of `ppm = 10`, all peaks within `mz[1] - ppm / 1e6` and `mz[2] + ppm / 1e6` are returned.
`type` | For `processHistory`: restrict returned `ProcessHistory` objects to analysis steps of a certain type. Use the `processHistoryTypes` to list all supported values. For `chromPeaks`: `character` specifying which peaks to return if `rt` or `mz` are defined. For `type = "any"` all chromatographic peaks that overlap the range defined by the `mz` or by the `rt`. For `type = "within"` only peaks completely within the range(s) are returned.
`adjusted` | logical(1) whether adjusted or raw (i.e. the original retention times reported in the files) should be returned.
`BPPARAM` | Parameter class for parallel processing. See `bpparam`.
`msLevel` | `integer(1)` defining the MS level on which the peak detection should be performed. Defaults to `msLevel = 1`.
`keepAdjustedRtime` | For `dropFeatureDefinitions,XCMSnExp`: `logical(1)` defining whether eventually present retention time adjustment should not be dropped. By default dropping feature definitions drops retention time adjustment results too.
`dropLastN` | For `dropFeatureDefinitions,XCMSnExp`: `numeric(1)` defining the number of peak grouping related process history steps to remove. By default `dropLastN = -1`, dropping the chromatographic peaks removes all process history steps related to peak grouping. Setting e.g. `dropLastN = 1` will only remove the most recent peak grouping related process history step.
`param` | A `CentWaveParam`, `MatchedFilterParam`, `MassifquantParam`, `MSWParam` or `CentWavePredIsoParam` object with the settings for the chromatographic peak detection algorithm.
`return.type` | Character specifying what type of object the method should return. Can be either `"XCMSnExp"` (default), `"list"` or `"xcmsSet"`.
`FUN` | For `spectrapply`: a function that should be applied to each spectrum in the object.

### Value

For `profMat`: a `list` with a the profile matrix `matrix` (or matrices if `fileIndex` was not specified or if `length(fileIndex) > 1`). See `profile-matrix` for general help and information about the profile matrix.

For `adjustedRtime`: if `bySample = FALSE` a `numeric` vector with the adjusted retention for each spectrum of all files/samples within the object. If `bySample = TRUE` a `list` (length equal to the number of samples) with adjusted retention times grouped by sample. Returns `NULL` if no adjusted retention times are present.

For `featureDefinitions`: a `DataFrame` with peak grouping information, each row corresponding to one mz-rt feature (grouped peaks within and across samples) and columns `"mzmed"` (median mz value), `"mzmin"` (minimal mz value), `"mzmax"` (maximum mz value), `"rtmed"` (median retention time), `"rtmin"` (minimal retention time), `"rtmax"` (maximal retention time) and `"peakidx"`. Column `"peakidx"` contains a `list` with indices of chromatographic peaks (rows) in the matrix returned by the `chromPeaks` method that belong to that feature group. The method returns `NULL` if no feature definitions are present.

For `chromPeaks`: if `bySample = FALSE` a `matrix` with at least the following columns: `"mz"` (intensity-weighted mean of mz values of the peak across scans/retention times), `"mzmin"` (minimal mz value), `"mzmax"` (maximal mz value), `"rt"` (retention time for the peak apex), `"rtmin"` (minimal retention time), `"rtmax"` (maximal retention time), `"into"` (integrated, original, intensity of the peak), `"maxo"` (maximum intentity of the peak), `"sample"` (sample index in which the peak was identified) and `"is_filled"` defining whether the chromatographic peak was identified by the peak picking algorithm (`0`) or was added by the `fillChromPeaks` method (`1`). Depending on the employed peak detection algorithm and the `verboseColumns` parameter of it additional columns might be returned. For `bySample = TRUE` the chronatographic peaks are returned as a `list` of matrices, each containing the chromatographic peaks of a specific sample. For samples in which no peaks were detected a matrix with 0 rows is returned.

For `rtime`: if `bySample = FALSE` a numeric vector with the retention times of each scan, if `bySample = TRUE` a `list` of numeric vectors with the retention times per sample.

For `mz`: if `bySample = FALSE` a `list` with the mz values (numeric vectors) of each scan. If `bySample = TRUE` a `list` with the mz values per sample.

For `intensity`: if `bySample = FALSE` a `list` with the intensity values (numeric vectors) of each scan. If `bySample = TRUE` a `list` with the intensity values per sample.

For `spectra`: if `bySample = FALSE` a `list` with `Spectrum` objects. If `bySample = TRUE` the result is grouped by sample, i.e. as a `list` of `lists`, each element in the outer `list` being the `list` of spectra of the specific file.

For `processHistory`: a `list` of `ProcessHistory` objects providing the details of the individual data processing steps that have been performed.

### Slots

`.processHistory`

  `list` with `XProcessHistory` objects tracking all individual analysis steps that have been performed.

`msFeatureData`

  `MsFeatureData` class extending `environment` and containing the results from a chromatographic peak detection (element `"chromPeaks"`), peak grouping (element `"featureDefinitions"`) and retention time correction (element `"adjustedRtime"`) steps. This object should not be manipulated directly.

### Note

The `"chromPeaks"` element in the `msFeatureData` slot is equivalent to the `@peaks` slot of the `xcmsSet` object, the `"featureDefinitions"` contains information from the `@groups` and `@groupidx` slots from an `xcmsSet` object.

### Author(s)

Johannes Rainer

### See Also

`xcmsSet` for the old implementation. `OnDiskMSnExp`, `MSnExp` and `pSet` for a complete list of inherited methods.

`findChromPeaks` for available peak detection methods returning a `XCMSnExp` object as a result.

`groupChromPeaks` for available peak grouping methods and `featureDefinitions` for the method to extract the feature definitions representing the peak grouping results. `adjustRtime` for retention time adjustment methods.

`chromatogram` to extract MS data as `Chromatogram` objects.

`extractMsData` for the method to extract MS data as `data.frame`s.

`fillChromPeaks` for the method to fill-in eventually missing chromatographic peaks for a feature in some samples.

### Examples

    ## Loading the data from 2 files of the faahKO package.
    library(faahKO)
    od <- readMSData(c(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
                       system.file("cdf/KO/ko16.CDF", package = "faahKO")),
                     mode = "onDisk")
    ## Now we perform a chromatographic peak detection on this data set using the
    ## matched filter method. We are tuning the settings such that it performs
    ## faster.
    mfp <- MatchedFilterParam(binSize = 6)
    xod <- findChromPeaks(od, param = mfp)

    ## The results from the peak detection are now stored in the XCMSnExp
    ## object
    xod

    ## The detected peaks can be accessed with the chromPeaks method.
    head(chromPeaks(xod))

    ## The settings of the chromatographic peak detection can be accessed with
    ## the processHistory method
    processHistory(xod)

    ## Also the parameter class for the peak detection can be accessed
    processParam(processHistory(xod)[[1]])

    ## The XCMSnExp inherits all methods from the pSet and OnDiskMSnExp classes
    ## defined in Bioconductor's MSnbase package. To access the (raw) retention
    ## time for each spectrum we can use the rtime method. Setting bySample = TRUE
    ## would cause the retention times to be grouped by sample
    head(rtime(xod))

    ## Similarly it is possible to extract the mz values or the intensity values
    ## using the mz and intensity method, respectively, also with the option to
    ## return the results grouped by sample instead of the default, which is
    ## grouped by spectrum. Finally, to extract all of the data we can use the
    ## spectra method which returns Spectrum objects containing all raw data.
    ## Note that all these methods read the information from the original input
    ## files and subsequently apply eventual data processing steps to them.
    mzs <- mz(xod, bySample = TRUE)
    length(mzs)
    lengths(mzs)

    ## The full data could also be read using the spectra data, which returns
    ## a list of Spectrum object containing the mz, intensity and rt values.
    ## spctr <- spectra(xod)
    ## To get all spectra of the first file we can split them by file
    ## head(split(spctr, fromFile(xod))[[1]])

    ############
    ## Filtering
    ##
    ## XCMSnExp objects can be filtered by file, retention time, mz values or
    ## MS level. For some of these filter preprocessing results (mostly
    ## retention time correction and peak grouping results) will be dropped.
    ## Below we filter the XCMSnExp object by file to extract the results for
    ## only the second file.
    xod_2 <- filterFile(xod, file = 2)
    xod_2

    ## Now the objects contains only the idenfified peaks for the second file
    head(chromPeaks(xod_2))

    head(chromPeaks(xod)[chromPeaks(xod)[, "sample"] == 2, ])

    ##########
    ## Coercing to an xcmsSet object
    ##
    ## We can also coerce the XCMSnExp object into an xcmsSet object:
    xs <- as(xod, "xcmsSet")
    head(peaks(xs))

[Package xcms version 3.0.2 Index]