newBrukerBAFReader {rtms}

Open a Bruker single-acquisition BAF directory

Description

Creates an RTMS reader object (of class rtmsBrukerBAFReader) which can extract data from a Bruker single acquisition directory (extension ".d")

Usage

newBrukerBAFReader(bafdir)

Arguments

bafdir

A directory (usually with the extension ".d") containing data from a single Bruker acquisition. This directory will contain a file with extension ".baf" that holds the primary raw data, as well as an index and calibration file (see Details).

Details

Currently, RTMS can create reader objects for two binary Bruker data formats, BAF (presumably standing for "Bruker acquisition format") holding data from a single spectrum acquisition, and MCF (probably "multiacquisition container format") containing data from multiple spectra acquired in a single run. Both formats hold data in a directory marked with the extension ".d". The single acquisition BAF format directory contains three essential data files: the main raw data file with extension ".baf", an index file with extension ".baf_idx", and a calibration data file with extension ".baf_xtr". This function processes the index and calibration files so that raw data can be extracted quickly on demand from the ".baf" file.

An important note: when a MCF multi-acquistion reader is created, it creates an open connection to the raw data file, which allows for quicker processing of many spectra in a single file. However, because a BAF file contains only a single spectrum, there is little advantage to maintaining an open connection, so the connection is re-opened every time data is read. Thus, while it is important to close an MCF reader object when all data is extracted, it is not necessary to close an object of class rtmsBrukerBAFReader.

Value

An object of class rtmsBrukerBAFReader which can extract raw data from the specified directory