FindPeaks {TargetSearch}R Documentation

Extract peaks from chromatogram files

Description

This function extracts the maximum intensity of a list of masses in a given RI window.

Usage

FindPeaks(my.files, refLib, columns = c("SPECTRUM", "RETENTION_TIME_INDEX"),
          showProgressBar = FALSE)

Arguments

my.files A character vector naming files to be searched.
refLib A numeric matrix with three columns. The second column contains the masses and the first and third column contains the RI limits.
columns A numeric vector with the positions of the columns 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.

Note

This is an internal function not intended to be invoked directly.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

medianRILib, sampleRI, peakFind, tsMSdata

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

my.files <- RIfiles(sampleDescription)
# make a three column matrix: lower RI, mass, upper RI
refLib   <- refLib(refLibrary)
head(refLib)

# extract the peaks
peaks <- FindPeaks(my.files, refLib)
    

[Package TargetSearch version 1.0.0 Index]