chromatogram,MSnExp-method {MSnbase} | R Documentation

## Extract chromatogram object(s)

### Description

The `chromatogram` method extracts chromatogram(s) from an `MSnExp` or `OnDiskMSnExp` object. Depending on the provided parameters this can be a total ion chromatogram (TIC), a base peak chromatogram (BPC) or an extracted ion chromatogram (XIC) extracted from each sample/file.

### Usage

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

### Arguments

`object` | For `chromatogram`: a `MSnExp` or `OnDiskMSnExp` object from which the chromatogram should be extracted.
`rt` | A `numeric(2)` or two-column `matrix` defining the lower and upper boundary for the retention time range/window(s) for the chromatogram(s). If a `matrix` is provided, a chromatogram is extracted for each row. If not specified, a chromatogram representing the full retention time range is extracted. See examples below for details.
`mz` | A `numeric(2)` or two-column `matrix` defining the mass-to-charge (mz) range(s) for the chromatogram(s). For each spectrum/retention time, all intensity values within this mz range are aggregated to result in the intensity value for the spectrum/retention time. If not specified, the full mz range is considered. See examples below for details.
`aggregationFun` | `character` defining the function to be used for intensity value aggregation along the mz dimension. Allowed values are `"sum"` (TIC), `"max"` (BPC), `"min"` and `"mean"`.
`missing` | `numeric(1)` allowing to specify the intensity value for if for a given retention time (spectrum) no signal was measured within the mz range. Defaults to `NA_real_`.
`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::bpparam()`.

### 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.

By default or if `mz` and/or `rt` are numeric vectors, the function extracts one `Chromatogram` object for each file in the `MSnExp` or `OnDiskMSnExp` object. Providing a numeric matrix with argument `mz` or `rt` enables to extract multiple chromatograms per file, one for each row in the matrix. If the number of columns of `mz` or `rt` are not equal to 2, `range` is called on each row of the matrix.

### Value

`chromatogram` returns a `Chromatograms` 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`). The 'featureData' of the returned object contains columns `"mzmin"` and `"mzmax"` with the values from input argument `mz` (if used) and `"rtmin"` and `"rtmax"` if the input argument `rt` was used.

### Author(s)

Johannes Rainer

### See Also

`Chromatogram` and `Chromatograms` for the classes that represent single and multiple chromatograms.

### Examples

    ## Read a test data file.
    library(msdata)
    f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
         system.file("microtofq/MM8.mzML", package = "msdata"))

    ## Read the data as an MSnExp
    msd <- readMSData(f, msLevel = 1)

    ## Extract the total ion chromatogram for each file:
    tic <- chromatogram(msd)

    tic

    ## Extract the TIC for the second file:
    tic[1, 2]

    ## Plot the TIC for the first file
    plot(rtime(tic[1, 1]), intensity(tic[1, 1]), type = "l",
        xlab = "rtime", ylab = "intensity", main = "TIC")

    ## Extract chromatograms for a MS data slices defined by retention time
    ## and mz ranges.
    rtr <- rbind(c(10, 60), c(280, 300))
    mzr <- rbind(c(140, 160), c(300, 320))
    chrs <- chromatogram(msd, rt = rtr, mz = mzr)

    ## Each row of the returned Chromatograms object corresponds to one mz-rt
    ## range. The Chromatogram for the first range in the first file is empty,
    ## because the retention time range is outside of the file's rt range:
    chrs[1, 1]

    ## The mz and/or rt ranges used are provided as featureData of the object
    fData(chrs)

    ## The mz method can be used to extract the m/z ranges directly
    mz(chrs)

    ## Also the Chromatogram for the second range in the second file is empty
    chrs[2, 2]

    ## Get the extracted chromatogram for the first range in the second file
    chr <- chrs[1, 2]
    chr

    plot(rtime(chr), intensity(chr), xlab = "rtime", ylab = "intensity")

[Package MSnbase version 2.12.0 Index]