plotFrags: plotFrags

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

plotFrags

Description

Plot the mass spectra from the profile matrix

Usage

plotFrags(object, sample, specID, normalize = TRUE, ...)

Arguments

object	an object of class "peaksDataset" where to keep the mass spectra; both abundance (y) than m/z (x)
sample	character, the sample from were to plot the mass spectra
specID	numerical, a vector containing the index of the spectra to be plotted.
normalize	logical, if TRUE normalize the intensity of the mass peak to 100, the most abundant is 100 consequetially
...	other parameter passed to the plot() function

Details

Plot the deconvoluted mass spectra from the profile matrix

Author(s)

[e-mail]

Examples

files <- list.files(path = paste(find.package("gcspikelite"), "data",
                    sep = "/"),"CDF", full = TRUE)
data <- peaksDataset(files[1:2], 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[1:2], data, settings = mfp)
data
## align two chromatogram
pA <- peaksAlignment(data@peaksdata[[1]], data@peaksdata[[2]],
                     data@peaksrt[[1]], data@peaksrt[[2]], D = 50,
                     metric = 3, compress = FALSE, type = 2, penality = 0.2)
pA@v$match
## plot the mass spectra
par(mfrow=c(2,1))
plotFrags(object=data, sample=1, specID=10)
plotFrags(object=data, sample=2, specID=12)

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