Read peak lists

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", "chromatotec", "asm"),
  pattern = NULL,
  peaktable_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw"),
  read_metadata = TRUE,
  progress_bar,
  cl = 1,
  data_format = NULL
)

Arguments

paths

Paths to files or folders containing peak list files.

find_files

Logical. Whether to treat the supplied paths as directories to search for files. Inferred if not supplied, by testing whether every path is a file.

format_in

Format of files to be imported/converted. One of chemstation (the default), shimadzu_fid, shimadzu_dad, shimadzu_lcd, shimadzu_gcd, chromatotec, or asm.

pattern

A pattern (e.g. a file extension). Defaults to NULL, in which case the file extension will be deduced from format_in.

peaktable_format

Whether to return peak tables in chromatographr or original format.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

read_metadata

Logical. Whether to attach metadata. 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 parallel workers to use or a cluster object created by makeCluster (a set of parallel R worker processes). Defaults to 1.

data_format

Deprecated. Use peaktable_format instead.

Value

A peak_list: a list with one element per sample, holding its peak table, or a list of peak tables named by signal where the file records more than one. Each row is a peak.

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
path <- "tests/testthat/testdata/RUTIN2.D"
peak_list <- read_peaklist(path)
peak_list[["RUTIN2"]][["254"]]
}