getBrukerMCFIntensities {rtms}

Retrieve peak intensities directly from an MCF file

Description

The size of mass spectrometric data in general, and Bruker MCF directories specifically, makes the extraction of data a resource intensive and time consuming process. rtms as a package is designed to reduce this burden, but pulling a sample set from an MCF file can (in the event of compressed spectra) requires reading nearly all data out of a file, which could take an extremely long time over a network connection. Since peak intensity (calculated as the sum of local intensity maxima within a given peak width) is one of the most common measurements used in evaluating spectra, and because this measure can be extracted without extracting the full spectra, this function aims to avoid expensive reading time by skipping the creation of a sample set object and calculating peak intensity directly. Other measurements are not possible, but full spectra do not have to be read, even when spectra are compressed, as local maxima are pre-processed and stored separately in a Bruker MCF file.

Usage

getBrukerMCFIntensities(reader, peaks, indices)

Arguments

reader

An RTMS reader object of class rtmsBrukerMCFReader

peaks

A list of peak objects of class rtmsPeak

indices

A vector of numeric indices specifying which acquisitions the measurements should be taken from

Value

A data frame containing columns specifying the index of each acquisition, the name of each acquistion (if indices is a named vector), the peak value of the peak measure, the peak name (if peaks is a named list), the measure name (which will always be "PeakIntensity"), and the measured value for that sample and peak. Format matches the output of measureSampleSet