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", "RETENTION_TIME"),
    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 positions of the columns SPECTRUM, RETENTION_TIME_INDEX, and RETENTION_TIME 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(TSExample)

# get RI file path
RI.path <- file.path(find.package("TargetSearchData"), "gc-ms-data")
refLibrary <- ImportLibrary(file.path(RI.path,"library.txt"))

# update RI file path
RIpath(sampleDescription) <- RI.path

peakData <- peakFind(sampleDescription, refLibrary, corRI)
# show peak Intensities. 
head(Intensity(peakData), 2)

# How to get intensities for a particular metabolite
# just select the identifier. Here extract the intensities
# for the first metabolite in the library
IntMatrix <- Intensity(peakData)[[1]]
[Package TargetSearch version 1.44.0 Index]