plotRIdev: Plot Retention Time Index Deviation

In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description

plotRIdev plots the Retention Time Index Deviation of a given set of metabolites. plotAllRIdev saves the plots of the RI deviations of all the metabolites in the library object into a PDF file.

Usage

plotRIdev(Lib, peaks, libId = 1)

plotAllRIdev(Lib, peaks, pdfFile, width = 8, height = 8, ...)

Arguments

Lib	A tsLib object created by ImportLibrary function.
peaks	A tsMSdata object. See peakFind.
libId	A numeric vector providing the indices of the metabolites to plot.
pdfFile	A file name where the plot will be saved. Only plotAllRIdev.
width, height	The width and height of the plots in inches. Only plotAllRIdev.
...	Further options passed to pdf.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

ImportLibrary, tsLib, tsMSdata, pdf

Examples

require(TargetSearchData)
data(TSExample)

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

peakData <- peakFind(sampleDescription, refLibrary, corRI)

# Plot RI deviation of metabolite "Valine"
grep("Valine", libName(refLibrary)) # answer: 3
plotRIdev(refLibrary, peakData, libId = 3)

# Plot an RI deviation overview of the first nine metabolites
plotRIdev(refLibrary, peakData, libId = 1:9)

# Save all RI deviation into a pdf file
plotAllRIdev(refLibrary, peakData, pdfFile = "RIdeviations.pdf")

TargetSearch documentation built on March 12, 2021, 2 a.m.