FindPeaks: Extract peaks from chromatogram files

In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description

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

Usage

FindPeaks(my.files, refLib, columns = NULL, showProgressBar = FALSE)

Arguments

my.files	A character vector naming RI files to be searched.
refLib	A numeric matrix with three columns or a list of three column matrices. The second column contains the masses and the first and third column contains the RI limits.
showProgressBar	Logical. Should the progress bar be displayed?
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.

Details

The reference library parameter refLib can be either a single three-column matrix or a list of such matrices. If it is a list, the length must match the length of my.files. In this case, every component will be used to iteratively search in the corresponding file.

The RI files format can be either "text" or "binary". The type is detected dinamically.

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

# load example CDF files
require(TargetSearchData)
# load pre-calculated example data and objects
data(TSExample)

# 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)
    

Example output

Loading required package: ncdf4
Loading required package: TargetSearchData
   minRI  mz  maxRI
1 218767  89 226767
1 218767 115 226767
1 218767 158 226767
1 218767 174 226767
1 218767 189 226767
2 224554  86 232554

TargetSearch documentation built on March 12, 2021, 2 a.m.