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

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.frames.

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))