specmine (version 4.0.0)

read_ms_spectra: 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 = ","
)

Value

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

xSet.

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.

Examples

if (FALSE) {
folder.name <- "path/to/folder/with/mzml_or_mzxml_files"
read_ms_spectra(folder.name, filename.meta = NULL)
}