chromatogram-method: Extracting chromatograms
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Details Value Note Author(s) See Also Examples

chromatogram: extract chromatographic data (such as an extracted ion chromatogram, a base peak chromatogram or total ion chromatogram) from an OnDiskMSnExp or XCMSnExp objects. See also the help page of the chromatogram function in the MSnbase package.

## S4 method for signature 'XCMSnExp'
chromatogram(
  object,
  rt,
  mz,
  aggregationFun = "sum",
  missing = NA_real_,
  msLevel = 1L,
  BPPARAM = bpparam(),
  adjustedRtime = hasAdjustedRtime(object),
  filled = FALSE,
  include = c("apex_within", "any", "none")
)

`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.
`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.
`aggregationFun`	`character(1)` specifying the function to be used to aggregate intensity values across the mz value range for the same retention time. Allowed values are `"sum"` (the default), `"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(1)` 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 Chromatograms 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.
`include`	`character(1)` defining which chromatographic peaks should be returned. Supported are `include = "apex_within"` (the default) which returns chromatographic peaks that have their apex within the `mz` `rt` range, `include = "any"` to return all chromatographic peaks which m/z and rt ranges overlap the `mz` and `rt` or `include = "none"` to not include any chromatographic peaks.

Arguments rt and mz allow to specify the MS data slice (i.e. the m/z range and retention time window) from which the chromatogram should be extracted. These parameters can be either a numeric of length 2 with the lower and upper limit, or a matrix with two columns with the lower and upper limits to extract multiple EICs at once. The parameter aggregationSum allows to specify the function to be used to aggregate the intensities across the m/z 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).

If for a given retention time no intensity is measured in that spectrum a NA intensity value is returned by default. This can be changed with the parameter missing, setting missing = 0 would result in a 0 intensity being returned in these cases.

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.

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 changed by setting adjustedRtime = FALSE.

Johannes Rainer

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`.

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

od <- readMSData(faahko_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(prefilter = c(3, 20000)))

## 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])