TargetSearch (version 1.28.1)

plotPeak: Plot peaks

Description

Plot a peak of a given metabolite in a given sample showing the search windows.

Usage

plotPeak(samples, Lib, metProf, rawpeaks, which.smp=1, which.met=1,
	massRange=NULL, corMass=FALSE)

Arguments

samples

A tsSample object created by ImportSamples function.

Lib

A tsLib object created by ImportLibrary function.

metProf

A metabolite profile object. See Profile

rawpeaks

A thre component list containing the retention time, the intensity matrix, and the mass range. See peakCDFextraction.

which.smp

A numeric value indicating the sample.

which.met

A numeric value indicating the metabolite.

massRange

A two component numeric vector with the scan mass range to extract. or NULL for automatic detection.

corMass

Logical. If TRUE, show only correlating masses for the selected metabolite. Show all masses otherwise.

Value

A two component list containing the retention time and the intensity matrices. This list can be recycled as the 'rawpeaks' parameter for further plots (for example in a loop), so the CDF file doesn't need to be read again.

See Also

plotPeakSimple, RIcorrect, tsMSdata, tsRim, peakCDFextraction, matplot

Examples

require(TargetSearchData)
data(TargetSearchData)

# update CDF and RI paths
CDFpath(sampleDescription) <- file.path(find.package("TargetSearchData"), "gc-ms-data")
RIpath(sampleDescription) <- file.path(find.package("TargetSearchData"), "gc-ms-data")

# Plot the peak "Valine" for sample number 1
grep("Valine", libName(refLibrary)) # answer: 3

# plot peak from the cdf file. The rawpeaks object can be recycled in order to plot
# other metabolites.
rawpeaks <- plotPeak(sampleDescription, refLibrary, metabProfile, which.smp=1,
        which.met=3, massRange=c(85,500), corMass=FALSE)