FindAllPeaks: Extract peaks from chromatogram files - low level function
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

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

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

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

`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.

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.

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.

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.

Alvaro Cuadros-Inostroza

FindPeaks, ri_data_extract,

# 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)