peakFind {TargetSearch}R Documentation

Intensities and RI matrices

Description

This function returns a list of the intensities and RI matrices that were searched.

Usage

peakFind(samples, Lib, cor_RI, columns = c("SPECTRUM", "RETENTION_TIME_INDEX"),
         showProgressBar = FALSE)

Arguments

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?

Value

A tsMSdata object.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

ImportSamples, ImportLibrary, medianRILib, sampleRI, tsMSdata, tsLib, tsSample

Examples

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]]


[Package TargetSearch version 1.0.0 Index]