Combine Spectra

Description

combineSpectra combines spectra in a MSnExp 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.

Usage

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

Arguments

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")