newBrukerMCFReader: Open a Bruker multi-acquisition MCF directory

In rtms: R Toolkit for Mass Spectrometry

Open a Bruker multi-acquisition MCF directory

Description

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

Usage

newBrukerMCFReader(mcfdir)

Arguments

mcfdir

A directory (usually with the extension ".d") containing data from a Bruker multi-acquisition run. This directory will contain a files with extenssion ".mcf" and matching index files with extension ".mcf_idx" (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 "multi-acquisition 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 multi-acquisition MCF format directory contains four essential data files: the main raw data file ending in "_1" with extension ".mcf", a matching index file with extension ".mcf_idx", and a calibration data file ending in "_2" with extension ".mcf", and the matching calibration index file with extension ".mcf_idx". This function preprocesses the main index file and calibration files so that raw data can be extracted quickly on demand from the main ".mcf" file.

An important note: when a MCF multi-acquisition 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. This connection will remain open until the reader is closed with the close function.

Value

A reader object of class rtmsBrukerMCFReader with an open connection to the main ".mcf" data file.

rtms documentation built on June 7, 2023, 5:59 p.m.