XCMSnExp-class: Data container storing xcms preprocessing results
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Value Slots Chromatographic peak data Adjusted retention times Correspondence results, features Note Author(s) See Also Examples

The XCMSnExp object is a container for the results of a G/LC-MS data preprocessing that comprises chromatographic peak detection, alignment and correspondence. These results can be accessed with the chromPeaks, adjustedRtime and featureDefinitions functions; see below (after the Usage, Arguments, Value and Slots sections) for more details). 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. XCMSnExp objects, by directly extending the OnDiskMSnExp object from the MSnbase package, inherit all of its functionality and allows thus an easy access to the full raw data at any stage of an analysis. To support interaction with packages requiring the old objects, XCMSnExp objects can be coerced into xcmsSet objects using the as method (see examples below). All preprocessing results will be passed along to the resulting xcmsSet object.

General functions for XCMSnExp objects are (see further below for specific function to handle chromatographic peak data, alignment and correspondence results):

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).

hasFilledChromPeaks: whether filled-in peaks are present or not.

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.

hasFilledChromPeaks: whether the object contains any filled-in chromatographic peaks.

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. The function supports also the parameter type that allows to specify which features to be returned if any of rt or mz is specified. For details see help of chromPeaks. See also featureSummary for a function to calculate simple feature summaries.

chromPeaks, chromPeaks<-: extract or set the matrix containing the information on identified chromatographic peaks. Rownames of the matrix represent unique IDs of the respective peaks within the experiment. 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, ppm and type allow to extract only chromatographic peaks overlapping the defined retention time and/or m/z ranges. Argument type allows to define how overlapping is determined: for type == "any" (the default), all peaks that are even partially overlapping the region are returned, for type == "within" the full peak has to be within the region and for type == "apex_within" the peak's apex position (highest signal of the peak) has to be within the region. 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. Also, chromPeaks<- will replace any existing chromPeakData.

chromPeakData and chromPeakData<- allow to get or set arbitrary chromatographic peak annotations. These are returned or ar returned as a DataFrame. Note that the number of rows and the rownames of the DataFrame have to match those of chromPeaks.

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 of 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 by default (with parameter add = FALSE) previous peak detection results are removed. Use add = TRUE to perform a second round of peak detection and add the newly identified peaks to the previous peak detection results. Correspondence results (features) are always removed prior to peak detection. 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.

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.

XCMSnExp objects can be combined with the c function. This combines identified chromatographic peaks and the objects' pheno data but discards alignment results or feature definitions.

plot plots the spectrum data (see plot for MSnExp objects in the MSnbase package for more details. For type = "XIC", identified chromatographic peaks will be indicated as rectangles with border color peakCol.

processHistoryTypes()

hasFilledChromPeaks(object)

## 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, msLevel = 1:20)

## S4 method for signature 'XCMSnExp'
hasChromPeaks(object, msLevel = 1:20)

## S4 method for signature 'XCMSnExp'
hasFilledChromPeaks(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 = c("any", "within", "apex_within"),
  msLevel = 1:20
)

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

## S4 method for signature 'XCMSnExp'
chromPeaks(
  object,
  bySample = FALSE,
  rt = numeric(),
  mz = numeric(),
  ppm = 0,
  msLevel = integer(),
  type = c("any", "within", "apex_within"),
  isFilledColumn = FALSE
)

## 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,
  add = FALSE
)

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

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

## S3 method for class 'XCMSnExp'
c(...)

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

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

## S4 method for signature 'XCMSnExp,missing'
plot(x, y, type = c("spectra", "XIC"), peakCol = "#ff000060", ...)

`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 `integer` specifying the index of the files/samples for which the `ProcessHistory` objects should be retrieved.
`...`	Additional parameters.
`msLevel`	`integer` specifying the MS level(s) for which identified chromatographic peaks should be returned.
`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 partially overlapping the range defined by `mz` and/or `rt` are returned, `type = "within"` returns only peaks completely within the region and `type = "apex_within"` peaks for which the peak's apex is within the region.
`isFilledColumn`	`logical(1)` whether a column `"is_filled"` is included in the returned `"matrix"` providing the information if a peak was filled in. Alternatively, this information would be provided by the `chromPeakData` data frame.
`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`.
`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"`.
`add`	For `findChromPeaks`: if newly identified chromatographic peaks should be added to the peak matrix with the already identified chromatographic peaks. By default (`add = FALSE`) previous peak detection results will be removed.
`FUN`	For `spectrapply`: a function that should be applied to each spectrum in the object.
`x`	For `plot`: `XCMSnExp` object.
`y`	For `plot`: not used.
`peakCol`	For `plot`: the color that should be used to indicate identified chromatographic peaks (only in combination with `type = "XIC"` and if chromatographic peaks are present).

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 (each row being a chromatographic peak, rownames representing unique IDs of the peaks) 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 of 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 Depending on the employed peak detection algorithm and the verboseColumns parameter of it, additional columns might be returned. If parameter isFilledColumn was set to TRUE a column named "is_filled" is also returned. For bySample = TRUE the chromatographic 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.

.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.

Chromatographic peak data is added to an XCMSnExp object by the findChromPeaks function. Functions to access chromatographic peak data are:

hasChromPeaks whether chromatographic peak data is available, see below for help of the function.
chromPeaks access chromatographic peaks (see below for help).
dropChromPeaks remove chromatographic peaks (see below for help).
dropFilledChromPeaks remove filled-in peaks (see below for help).
fillChromPeaks fill-in missing peaks (see respective help page).
plotChromPeaks plot identified peaks for a file (see respective help page).
plotChromPeakImage plot distribution of peaks along the retention time axis (see respective help page).
highlightChromPeaks add chromatographic peaks to an existing plot of a Chromatogram (see respective help page).

Adjusted retention times are stored in an XCMSnExp object besides the original, raw, retention times, allowing to switch between raw and adjusted times. It is also possible to replace the raw retention times with the adjusted ones with the applyAdjustedRtime. The adjusted retention times are added to an XCMSnExp by the adjustRtime function. All functions related to the access of adjusted retention times are:

hasAdjustedRtime whether adjusted retention times are available (see below for help).
dropAdjustedRtime remove adjusted retention times (see below for help).
applyAdjustedRtime replace the raw retention times with the adjusted ones (see respective help page).
plotAdjustedRtime plot differences between adjusted and raw retention times (see respective help page).

The correspondence analysis (groupChromPeaks) adds the feature definitions to an XCMSnExp object. All functions related to these are listed below:

hasFeatures whether correspondence results are available (see below for help).
featureDefinitions access the definitions of the features (see below for help).
dropFeatureDefinitions remove correspondence results (see below for help).
featureValues access values for features (see respective help page).
featureSummary perform a simple summary of the defined features (see respective help page).
overlappingFeatures identify features that are overlapping or close in the m/z - rt space (see respective help page).
quantify extract feature intensities and put them, along with feature definitions and phenodata information, into a SummarizedExperiment. See help page for details.

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.

Johannes Rainer

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.

as (as(x, "data.frame")) in the MSnbase package for the method to extract MS data as data.frames.

featureSummary to calculate basic feature summaries.

featureChromatograms to extract chromatograms for each feature.

chromPeakSpectra to extract MS2 spectra with the m/z of the precursor ion within the m/z range of a peak and a retention time within its retention time range.

featureSpectra to extract MS2 spectra associated with identified features.

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

## 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))