| plotPeak {TargetSearch} | R Documentation |
Plot selected ions in a given time range.
plotPeak(rawpeaks, time.range, masses, cdfFile = NULL, useRI = FALSE,
rimTime = NULL, standard = NULL, massRange = c(85, 500), ...)
rawpeaks |
A two component list containing the retention time and the intensity matrices.
See peakCDFextraction. |
time.range |
The time range to plot in retention time or retention time index units to plot. |
masses |
A vector containing the ions or masses to plot. |
cdfFile |
The name of a CDF file. If a file name is specified, the ions will be extracted
from there instead of using rawpeaks. |
useRI |
Logical. Whether to use Retention Time Indices or not. |
rimTime |
A retention time matrix of the found retention time markers. It is only used
when useRI is TRUE. |
standard |
A numeric vector with RI values of retention time markers. It is only used
when useRI is TRUE. |
massRange |
A two component numeric vector with the scan mass range to extract. |
... |
Further options passed to matplot. |
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
RIcorrect, tsMSdata, tsRim,
peakCDFextraction, matplot
require(TargetSearchData)
data(TargetSearchData)
# update CDF path
CDFpath(sampleDescription) <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
# Plot the peak "Valine" for sample number 1
grep("Valine", libName(refLibrary)) # answer: 3
# select the first file
cdfFile <- CDFfiles(sampleDescription)[1]
# select "Valine" top masses
top.masses <- topMass(refLibrary)[[3]]
# plot peak from the cdf file
plotPeak(cdfFile = cdfFile, time.range = libRI(refLibrary)[3] + c(-2000,2000),
masses = top.masses, useRI = TRUE, rimTime = RImatrix[,1],
standard = rimStandard(rimLimits), massRange = c(85, 500))
# the same, but extracting the peaks into a list first. This may be better if
# you intend to loop through several peaks.
rawpeaks <- peakCDFextraction(cdfFile, massRange = c(85,500))
plotPeak(rawpeaks, time.range = libRI(refLibrary)[3] + c(-2000,2000),
masses = top.masses, useRI = TRUE, rimTime = RImatrix[,1],
standard = rimStandard(rimLimits), massRange = c(85, 500))