plotAlignedFrags: plotAlignedFrags

In rromoli/flagme: Analysis of Metabolomics GC/MS Data

plotAlignedFrags

Description

Plot the aligned mass spectra

Usage

plotAlignedFrags(
  object,
  outList,
  specID,
  fullRange = TRUE,
  normalize = TRUE,
  ...
)

Arguments

object	where to keep the mass range of the experiment
outList	where to keep the mass spectra; both abundance than m/z
specID	a vector containing the index of the spectra to be plotted. Is referred to outList
fullRange	if TRUE uses the mass range of the whole experiment, otherwise uses only the mass range of each plotted spectum
normalize	if TRUE normalize the intensity of the mass peak to 100, the most abundant is 100% and the other peaks are scaled consequetially
...	further arguments passed to the ‘plot’ command

Details

Plot the deconvoluted and aligned mass spectra collected using gatherInfo()

Author(s)

Riccardo Romoli ([e-mail])

Examples

files <- list.files(path = paste(find.package("gcspikelite"), "data",
                    sep = "/"),"CDF", full = TRUE)
data <- peaksDataset(files[1:4], mz = seq(50, 550), rtrange = c(7.5, 8.5))
## create settings object
mfp <- xcms::MatchedFilterParam(fwhm = 10, snthresh = 5)
cwt <- xcms::CentWaveParam(snthresh = 3, ppm = 3000, peakwidth = c(3, 40),
 prefilter = c(3, 100), fitgauss = FALSE, integrate = 2, noise = 0,
 extendLengthMSW = TRUE, mzCenterFun = "wMean")
data <- addXCMSPeaks(files[1:4], data, settings = mfp)
data
## multiple alignment
ma <- multipleAlignment(data, c(1,1,2,2), wn.gap = 0.5, wn.D = 0.05,
 bw.gap = 0.6, bw.D = 0.2, usePeaks = TRUE, filterMin = 1, df = 50,
 verbose = TRUE, metric = 2, type = 2)

## gather apex intensities
gip <- gatherInfo(data, ma)
gip[[33]]
plotAlignedFrags(object = data, outList = gip, specID = 33)

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.