specmine (version 4.0.0)

read_dataset_dx: 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
)

Value

A dataset object created from the spectra found in folder.data

and the optional metadata file.

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.

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)
if (FALSE) {
read_dataset_dx(folder, filename.meta = meta_file)
}