peakFind: Intensities and RI matrices
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Value Author(s) See Also Examples

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

1	peakFind(samples, Lib, cor_RI, columns = NULL, 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`	Either `NULL`, a `character` vector, or an `integer` vector. In most cases, leave it as `NULL`. This parameter is used to configure the column names or positions of RI text files. See the documentation on the `text2bin` function for further details.
`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(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]]