chromatogram-method: Extracting chromatograms

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

Extracting chromatograms

Description

chromatogram: the method allows to extract chromatograms from OnDiskMSnExp and XCMSnExp objects. See also the chromatogram implementation for OnDiskMSnExp in the MSnbase package.

Usage

## S4 method for signature 'XCMSnExp'
chromatogram(object, rt, mz, aggregationFun = "sum",
  missing = NA_real_, msLevel = 1L, BPPARAM = bpparam(),
  adjustedRtime = hasAdjustedRtime(object), filled = FALSE)

Arguments

object	Either a OnDiskMSnExp or XCMSnExp object from which the chromatograms should be extracted.
rt	numeric(2) or two-column matrix defining the lower and upper boundary for the retention time range(s). If not specified, the full retention time range of the original data will be used. It is also possible to submit a numeric(1) in which case range is called on it to transform it to a numeric(2).
mz	numeric(2) or two-column matrix defining the lower and upper mz value for the MS data slice(s). If not specified, the chromatograms will be calculated on the full mz range. It is also possible to submit a numeric(1) in which case range is called on it to transform it to a numeric(2).
aggregationFun	character specifying the function to be used to aggregate intensity values across the mz value range for the same retention time. Allowed values are "sum", "max", "mean" and "min".
missing	numeric(1) allowing to specify the intensity value to be used if for a given retention time no signal was measured within the mz range of the corresponding scan. Defaults to NA_real_ (see also Details and Notes sections below). Use missing = 0 to resemble the behaviour of the getEIC from the old user interface.
msLevel	integer specifying the MS level from which the chromatogram should be extracted. Defaults to msLevel = 1L.
BPPARAM	Parallelisation backend to be used, which will depend on the architecture. Default is BiocParallel::bparam().
adjustedRtime	For chromatogram,XCMSnExp: whether the adjusted (adjustedRtime = TRUE) or raw retention times (adjustedRtime = FALSE) should be used for filtering and returned in the resulting Chromatogram object. Adjusted retention times are used by default if available.
filled	logical(1) whether filled-in peaks should also be returned. Defaults to filled = FALSE, i.e. returns only detected chromatographic peaks in the result object.

Details

Arguments rt and mz allow to specify the MS data slice from which the chromatogram should be extracted. The parameter aggregationSum allows to specify the function to be used to aggregate the intensities across the mz range for the same retention time. Setting aggregationFun = "sum" would e.g. allow to calculate the total ion chromatogram (TIC), aggregationFun = "max" the base peak chromatogram (BPC). The length of the extracted Chromatogram object, i.e. the number of available data points, corresponds to the number of scans/spectra measured in the specified retention time range. If in a specific scan (for a give retention time) no signal was measured in the specified mz range, a NA_real_ is reported as intensity for the retention time (see Notes for more information). This can be changed using the missing parameter.

Value

chromatogram returns a XChromatograms object with the number of columns corresponding to the number of files in object and number of rows the number of specified ranges (i.e. number of rows of matrices provided with arguments mz and/or rt). All chromatographic peaks with their apex position within the m/z and retention time range are also retained as well as all feature definitions for these peaks.

Note

Chromatogram objects extracted with chromatogram contain NA_real_ values if, for a given retention time, no signal was measured in the specified mz range. If no spectrum/scan is present in the defined retention time window a Chromatogram object of length 0 is returned.

For XCMSnExp objects, if adjusted retention times are available, the chromatogram method will by default report and use these (for the subsetting based on the provided parameter rt). This can be overwritten with the parameter adjustedRtime.

Author(s)

Johannes Rainer

See Also

XCMSnExp for the data object. Chromatogram for the object representing chromatographic data.

XChromatograms for the object allowing to arrange multiple XChromatogram objects.

plot to plot a XChromatogram or Chromatograms objects.

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

Examples

## Read some files from the faahKO package.
library(xcms)
library(faahKO)
faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
                    system.file('cdf/KO/ko16.CDF', package = "faahKO"),
                    system.file('cdf/KO/ko18.CDF', package = "faahKO"))

od <- readMSData(faahko_3_files, mode = "onDisk")

## Subset to speed up processing
od <- filterRt(od, rt = c(2500, 3000))

## Perform peak detection using default CentWave parameters
xod <- findChromPeaks(od, param = CentWaveParam())

## Extract the ion chromatogram for one chromatographic peak in the data.
chrs <- chromatogram(xod, rt = c(2700, 2900), mz = 335)

chrs

## Plot the chromatogram
plot(chrs)

## Extract chromatograms for multiple ranges.
mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
rtr <- matrix(c(2700, 2900, 2600, 2750), ncol = 2, byrow = TRUE)
chrs <- chromatogram(xod, mz = mzr, rt = rtr)

chrs <- chromatogram(xod, mz = mzr)

rtr[1, 1] <- 2785
chrs <- chromatogram(xod, mz = mzr, rt = rtr)

chrs

## Plot the extracted chromatograms
plot(chrs)

## Get access to all chromatograms for the second mz/rt range
chrs[1, ]

## Plot just that one
plot(chrs[1, , drop = FALSE])

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.