FindAllPeaks {TargetSearch}

R Documentation

Extract peaks from chromatogram files - low level function

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

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. It must be a scalar.
dev	The allowed retention index (RI) deviation or NULL. See details below.
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 dev parameter can either be NULL (as stated above), or a numeric vector. If the length is equal to 1, then the RI search window is the given RI plus or minus dev. If the length is 2, then the search window is from RI + dev[1] to RI + dev[2]. Note than in this case dev[1] is usually a negative value. An error is raised if the length is greater than 2

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 users.

In the future it may 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

# 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)

# an asymmetric deviation search
peaks <- FindAllPeaks(sampleDescription, refLibrary, 'GC.3', dev=c(-1000, 2000))
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)

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