Read All Spectra from a Directory — ls_read_dir • libscanR

Batch-imports spectrum files from a directory into a libs_dataset.

Usage

ls_read_dir(
  dir,
  pattern = "\\.(csv|tsv|txt)$",
  recursive = FALSE,
  sample_info = NULL,
  ...
)

Arguments

dir: Character. Directory path.
pattern: Character. File pattern (regex). Default "\\.(csv|tsv|txt)$".
recursive: Logical. Recurse into subdirectories. Default FALSE.
sample_info: data.frame/tibble. Optional sample metadata table. Must have a sample_id column matching (or being a subset of) the filenames without extension. Default NULL.
...: Additional arguments passed to ls_read_spectrum().

Value

A libs_dataset object.

Examples

dir <- tempfile()
dir.create(dir)
for (i in 1:3) {
  wl <- seq(200, 900, length.out = 100)
  int <- exp(-((wl - 393)^2) / 2) + stats::rnorm(100, 0, 0.01)
  utils::write.csv(data.frame(w = wl, i = int),
                   file.path(dir, paste0("s", i, ".csv")),
                   row.names = FALSE)
}
ds <- ls_read_dir(dir, verbose = FALSE)
unlink(dir, recursive = TRUE)