read_dataset_dx: Read a dataset from JDX files

In specmine: Metabolomics and Spectral Data Analysis and Mining

Read a dataset from JDX files

Description

Reads all JDX spectra files in a folder, combines their intensity values into a data matrix, and optionally attaches sample metadata.

Usage

read_dataset_dx(
  folder.data,
  filename.meta = NULL,
  type = "undefined",
  description = "",
  label.x = NULL,
  label.values = NULL,
  header.col.meta = TRUE,
  header.row.meta = TRUE,
  sep.meta = ",",
  verbose = TRUE
)

Arguments

folder.data	Path to the folder containing JDX files.
filename.meta	Optional metadata CSV file.
type	Character string describing the dataset type.
description	Character string with a dataset description.
label.x	Optional x-axis label.
label.values	Optional value labels.
header.col.meta	Logical; whether the metadata file has a header row.
header.row.meta	Logical; whether the metadata file has a row names column.
sep.meta	Field separator used in the metadata file.
verbose	Logical; whether progress messages should be shown.

Value

A dataset object created from the spectra found in folder.data and the optional metadata file.

Examples

folder <- tempdir()
meta_file <- tempfile(fileext = ".csv")
metadata_in <- data.frame(sample = c("sample1", "sample2"), class = c("A", "B"))
utils::write.csv(metadata_in, meta_file, row.names = FALSE)
## Not run: 
read_dataset_dx(folder, filename.meta = meta_file)

## End(Not run)

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