read_peaklist: Read peak lists

In ethanbass/chromConverter: Chromatographic File Converter

Read peak lists

Description

Reads peak lists from specified folders or vector of paths.

Usage

read_peaklist(
  paths,
  find_files,
  format_in = c("chemstation", "shimadzu_fid", "shimadzu_dad", "shimadzu_lcd",
    "shimadzu_gcd"),
  pattern = NULL,
  data_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw"),
  read_metadata = TRUE,
  progress_bar,
  cl = 1
)

Arguments

paths	paths to files or folders containing files.
find_files	Logical. Set to TRUE (default) if you are providing the function with a folder or vector of folders containing the files. Otherwise, set toFALSE.
format_in	Format of files to be imported/converted. Current options include: chemstation, shimadzu_fid, shimadzu_dad, shimadzu_lcd, and shimadzu_gcd.
pattern	pattern (e.g. a file extension). Defaults to NULL, in which case file extension will be deduced from format_in.
data_format	Either chromatographr or original.
metadata_format	Format to output metadata. Either chromconverter or raw.
read_metadata	Logical, whether to attach metadata (if it's available). Defaults to TRUE.
progress_bar	Logical. Whether to show progress bar. Defaults to TRUE if pbapply is installed.
cl	Argument to pbapply specifying the number of clusters to use or a cluster object created by makeCluster. Defaults to 1.

Value

A list of chromatograms in matrix or data.frame format, according to the value of format_out.

Author(s)

Ethan Bass

Examples

path <- "tests/testthat/testdata/dad1.uv"
chr <- read_chroms(path, find_files = FALSE, format_in = "chemstation_uv")

ethanbass/chromConverter documentation built on Jan. 14, 2025, 2:11 a.m.