combineSpectra,MSnExp-method {MSnbase} | R Documentation

## Combine Spectra

### Description

`combineSpectra` combines spectra in a MSnExp, OnDiskMSnExp or Spectra object applying the summarization function `fun` to sets of spectra defined by a factor (`fcol` parameter). The resulting combined spectrum for each set contains metadata information (present in `mcols` and all spectrum information other than `mz` and `intensity`) from the first spectrum in each set.

Combining of spectra for MSnExp or OnDiskMSnExp objects is performed by default for each file separately, combining of spectra across files is thus not possible. See examples for details.

### Usage

    ## S4 method for signature 'MSnExp'
    combineSpectra(object, fcol = "fileIdx",
      method = meanMzInts, ..., BPPARAM = bpparam())

    ## S4 method for signature 'Spectra'
    combineSpectra(object, fcol, method = meanMzInts,
      fun, ...)

### Arguments

`object` | A MSnExp or Spectra
`fcol` | For `Spectra` objects: `mcols` column name to be used to define the sets of spectra to be combined. If missing, all spectra are considered to be one set. For `MSnExp`/`OnDiskMSnExp` objects: column in `fData(object)` defining which spectra to combine. See examples below for more details.
`method` | `function` to be used to combine the spectra by `fcol`. Has to be a function that takes a list of spectra as input and returns a single Spectrum. See `meanMzInts()` for details.
`...` | additional arguments for `fun`.
`BPPARAM` | For `MSnExp`/`OnDiskMSnExp` objects: parallel processing setup to perform per-file parallel spectra combining. See `bpparam()` for more details.
`fun` | Deprecated use `method` instead.

### Value

A `Spectra` or `MSnExp` object with combined spectra. Metadata (`mcols`) and all spectrum attributes other than `mz` and `intensity` are taken from the first `Spectrum` in each set.

### Author(s)

Johannes Rainer, Laurent Gatto

### See Also

`meanMzInts()` for a function to combine spectra.

### Examples

    set.seed(123)
    mzs <- seq(1, 20, 0.1)
    ints1 <- abs(rnorm(length(mzs), 10))
    ints1[11:20] <- c(15, 30, 90, 200, 500, 300, 100, 70, 40, 20) # add peak
    ints2 <- abs(rnorm(length(mzs), 10))
    ints2[11:20] <- c(15, 30, 60, 120, 300, 200, 90, 60, 30, 23)
    ints3 <- abs(rnorm(length(mzs), 10))
    ints3[11:20] <- c(13, 20, 50, 100, 200, 100, 80, 40, 30, 20)

    ## Create the spectra.
    sp1 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
        intensity = ints1, rt = 1)
    sp2 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
        intensity = ints2, rt = 2)
    sp3 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.009),
        intensity = ints3, rt = 3)

    spctra <- Spectra(sp1, sp2, sp3,
        elementMetadata = DataFrame(idx = 1:3, group = c("b", "a", "a")))

    ## Combine the spectra reporting the maximym signal
    res <- combineSpectra(spctra, mzd = 0.05, intensityFun = max)
    res

    ## All values other than m/z and intensity are kept from the first spectrum
    rtime(res)

    ## Plot the individual and the merged spectrum
    par(mfrow = c(2, 1), mar = c(4.3, 4, 1, 1))
    plot(mz(sp1), intensity(sp1), xlim = range(mzs[5:25]), type = "h", col = "red")
    points(mz(sp2), intensity(sp2), type = "h", col = "green")
    points(mz(sp3), intensity(sp3), type = "h", col = "blue")
    plot(mz(res[[1]]), intensity(res[[1]]), type = "h",
        col = "black", xlim = range(mzs[5:25]))

    ## Combine spectra in two sets.
    res <- combineSpectra(spctra, fcol = "group", mzd = 0.05)
    res

    rtime(res)

    ## Plot the individual and the merged spectra
    par(mfrow = c(3, 1), mar = c(4.3, 4, 1, 1))
    plot(mz(sp1), intensity(sp1), xlim = range(mzs[5:25]), type = "h", col = "red")
    points(mz(sp2), intensity(sp2), type = "h", col = "green")
    points(mz(sp3), intensity(sp3), type = "h", col = "blue")
    plot(mz(res[[1]]), intensity(res[[1]]), xlim = range(mzs[5:25]), type = "h",
        col = "black")
    plot(mz(res[[2]]), intensity(res[[2]]), xlim = range(mzs[5:25]), type = "h",
        col = "black")

    ## Combining spectra of an MSnExp/OnDiskMSnExp objects
    ## Reading data from 2 mzML files
    sciex <- readMSData(dir(system.file("sciex", package = "msdata"),
        full.names = TRUE), mode = "onDisk")

    ## Filter the file to a retention time range from 2 to 20 seconds (to reduce
    ## execution time of the example)
    sciex <- filterRt(sciex, rt = c(2, 20))
    table(fromFile(sciex))

    ## We have thus 64 spectra per file.

    ## In the example below we combine spectra measured in one second to a
    ## single spectrum. We thus first define the grouping variable and add that
    ## to the `fData` of the object. For combining, we use the
    ## `consensusSpectrum` function that combines the spectra keeping only peaks
    ## that were found in 50% of the spectra; by defining `mzd = 0.01` all peaks
    ## within an m/z of 0.01 are evaluated for combining.
    seconds <- round(rtime(sciex))
    head(seconds)
    fData(sciex)$second <- seconds

    res <- combineSpectra(sciex, fcol = "second", mzd = 0.01, minProp = 0.1,
        method = consensusSpectrum)
    table(fromFile(res))

    ## The data was reduced to 19 spectra for each file.

[Package MSnbase version 2.12.0 Index]