| peakFind {TargetSearch} | R Documentation |
This function returns a list of the intensities and RI matrices that were searched.
peakFind(samples, Lib, cor_RI, columns = c("SPECTRUM", "RETENTION_TIME_INDEX"),
showProgressBar = FALSE)
samples |
A tsSample object created by ImportSamples function. |
Lib |
A tsLib object created by ImportLibrary function with
corrected RI values. See medianRILib. |
cor_RI |
A matrix of correlating selective masses RI for every sample.
See sampleRI. |
columns |
A numeric vector with the column positions of SPECTRUM and
RETENTION_TIME_INDEX or a character vector with the header names of those
columns. |
showProgressBar |
Logical. Should the progress bar be displayed? |
A tsMSdata object.
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
ImportSamples, ImportLibrary, medianRILib,
sampleRI, tsMSdata, tsLib,
tsSample
require(TargetSearchData)
data(TargetSearchData)
# 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)
# show peak Intensities.
head(Intensity(peakData))
# How to get intensities for a particular metabolite
#
# make a library index using top masses
libId <- libId(refLibrary, sel = FALSE)
# get the peak intensities of Metabolite 1, for example, of every mass
int.1 <- Intensity(peakData)[libId == 1,]
# this assigns the mass values to the row names of int.1
rownames(int.1) <- topMass(refLibrary)[[1]]