read_ms_spectra: Auto-exported function: read_ms_spectra

In specmine: Metabolomics and Spectral Data Analysis and Mining

Auto-exported function: read_ms_spectra

Description

Auto-exported function: read_ms_spectra

Usage

read_ms_spectra(
  folder.name,
  type = "undefined",
  filename.meta = NULL,
  description = "",
  prof.method = "bin",
  fwhm = 30,
  bw = 30,
  intvalue = "into",
  header.col.meta = TRUE,
  header.row.meta = TRUE,
  sep.meta = ","
)

Arguments

folder.name	Path to the folder containing LC/GC-MS raw files.
type	Dataset type.
filename.meta	Optional metadata filename.
description	Dataset description.
prof.method	Profiling method passed to xcms::xcmsSet().
fwhm	Full width at half maximum used by xcms.
bw	Bandwidth used for grouping peaks.
intvalue	Intensity value extracted from xcms peak groups.
header.col.meta	Logical indicating whether metadata has column headers.
header.row.meta	Logical indicating whether metadata has row headers.
sep.meta	Metadata field separator.

Value

A dataset object containing the processed LC/GC-MS spectra, the sample metadata if provided, and the associated xcms object in xSet.

Examples

## Not run: 
folder.name <- "path/to/folder/with/mzml_or_mzxml_files"
read_ms_spectra(folder.name, filename.meta = NULL)

## End(Not run)

specmine documentation built on Aug. 5, 2026, 5:06 p.m.