FindAllPeaks: Extract peaks from chromatogram files - low level function

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

This function extracts all peaks of a given metabolite in a given RI window. This function is intended for fine-tuning metabolite search parameters.

Usage

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FindAllPeaks(samples, Lib, libID, dev=NULL, mz=NULL, RI=NULL,
         mz_type = c('selMass', 'quantMass', 'topMass'),
         columns = NULL)

Arguments

samples

A tsSample object created by ImportSamples function.

Lib

A tsLib object created by ImportLibrary function.

libID

An index (integer or character) value representing the respective metabolite in the reference library Lib.

dev

The allowed retention index (RI) deviation or NULL.

mz

A list of m/z values to search or NULL.

RI

The expected retention index or NULL.

mz_type

whether to search for the selective, quant or top masses of the respective metabolite.

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 function searches for all peaks of a metabolite in all samples within a RI window. The parameters dev, mz, and RI have preference over the settings of the metabolite indexed by libID. In fact, if all of these parameters are not NULL, then refLib and libID are not used.

The columns parameter is only needed for custom text RI files. There is no need to change it.

Value

It returns a matrix in which each row represent a hit. Note that there can be zero rows if no hits are found. The columns are named and these are:

Int

Peak intensity

RI

Retention Index

RI

Retention Time

mz

the searched m/z value

fid

the respective file or sample index. An integer value.

Note

This is an internal function not intended to be invoked directly, but it is exposed for convenience and advanced used.

In the future it will replace FindPeaks.

See also the function ri_data_extract which offers a similar functionality but with different input parameters.

Author(s)

Alvaro Cuadros-Inostroza

See Also

FindPeaks, ri_data_extract,

Examples

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

# get and set the RI file path
RIpath(sampleDescription) <- file.path(find.package("TargetSearchData"), "gc-ms-data")

# search all peaks of Valine (GC.3) and selective masses
peaks <- FindAllPeaks(sampleDescription, refLibrary, 'GC.3')
head(peaks)

# a numeric index is also allowed
peaks <- FindAllPeaks(sampleDescription, refLibrary, 3)
head(peaks)

# search arbitrary masses at arbitrary RI. the reference library and ID
# must be set set to NULL.
peaks <- FindAllPeaks(sampleDescription, NULL, NULL, dev=3000, RI=270000, mz=c(144, 100))
head(peaks)

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