readBruker: Importing 1D NMR spectra from Bruker

In kimsche/MetaboMate: All you need for NMR-based metabolic profiling with R!

Description

Reading-in 1D NMR spectra in Bruker file format. The function recursively descends the directory tree of a given location and is searching for corresponding processing status (procs), acquisition status (acqus) and spectrum (r1) files.

Usage

readBruker(path, filter = T)

Arguments

path	A character string, specifying the path of the experiment folder location.
filter	Logical - if set to TRUE, then experiments with matching acqus, procs and 1r files are read-in, ignored are corrupt file systems and 2D experiments. If set to FALSE, the algorithm will abort if a file system is corrupt or if 2D experiments are present. Generally, the filter=TRUE option should be preferred except for some file system testing operations.

Details

The columns in meta represent spectrometer meta-variables and prefix a and p indicate if a parameter was extracted from the acquisition status (acqus) or processing status (procs) file, respectively. Parameter names without prefix were calculated on the fly (eg run-order). Spectrometer variables that often are of interest to s specific study include a_NS (number of scans), a_RG (receiver gain), a_Date (acquisition date), p_SF (spectrometer frequency) and a_AUNM (AU program). Further information can be found in Bruker's acquisition and processing manual.

Value

The following variables are automatically returned as globally defined workspace variables:

X

two-dimensional NMR matrix with spectra in rows and chemical shift variables in columns.

ppm

chemical shift vector (ppm).

meta

spectrometer metadata extracted from acqus and procs files (eg time of spectral acquisition).

Author(s)

Torben Kimhofer [e-mail]

Examples

path=system.file('extdata/', package = 'MetaboMate')
readBruker(path)

kimsche/MetaboMate documentation built on Aug. 8, 2020, 1:14 a.m.