Read Chromatograms

Reads chromatograms from specified folders or vector of paths using either an internal parser or bindings to an external library, such as Aston, Entab, ThermoRawFileParser, OpenChrom, rainbow.

Usage

read_chroms(
  paths,
  format_in = c("agilent_d", "agilent_dx", "asm", "chemstation", "chemstation_fid",
    "chemstation_ch", "chemstation_csv", "chemstation_ms", "chemstation_uv",
    "masshunter_dad", "chromeleon_uv", "chromatotec", "mzml", "mzxml", "mdf",
    "shimadzu_ascii", "shimadzu_dad", "shimadzu_fid", "shimadzu_gcd", "shimadzu_qgd",
    "shimadzu_lcd", "thermoraw", "varian_sms", "waters_arw", "waters_raw", "msd", "csd",
    "wsd", "csv", "other"),
  find_files,
  pattern = NULL,
  parser = c("", "chromconverter", "aston", "entab", "thermoraw", "openchrom", "rainbow"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  path_out = NULL,
  export_format = c("", "csv", "chemstation_csv", "cdf", "mzml", "animl", "arw"),
  force = FALSE,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  progress_bar,
  cl = 1,
  verbose = getOption("verbose"),
  sample_names = c("basename", "sample_name"),
  dat = NULL,
  ...
)

Arguments

paths

Paths to data files or directories containing the files.

format_in

Format of files to be imported/converted. Current options include: agilent_d, agilent_dx, chemstation, chemstation_uv, chemstation_ch, chemstation_csv, chemstation_ms, masshunter, masshunter_dad, chromeleon_uv, shimadzu_ascii, shimadzu_fid, shimadzu_dad, thermoraw, waters_arw, waters_raw, mzml, mzxml, cdf, mdf, msd, csd, wsd, or other.

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 to FALSE.

pattern

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

parser

What parser to use (optional). Current option are chromconverter, aston,, entab, thermoraw, openchrom, rainbow.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

Whether to output data in wide or long format. Either wide (default) or long.

path_out

Path for exporting files. If path is not specified, the user will be prompted to create a temp directory.

export_format

Export format. Currently the options include .csv, chemstation_csv (utf-16 encoding), cdf, mzml, animl and arw.

force

Logical. Whether to overwrite files when exporting. Defaults to FALSE.

read_metadata

Logical, whether to attach metadata (if it's available). Defaults to TRUE.

metadata_format

Format to output metadata. Either chromconverter or raw.

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.

verbose

Logical. Whether to print output from external parsers to the R console.

sample_names

Which sample names to use. Options are basename to use the filename (default) or sample_name to use the sample name encoded in the file metadata.

dat

Existing list of chromatograms to append results. Defaults to NULL.

...

Additional arguments to parser.

Value

A list of chromatograms in matrix, data.frame, or data.table format, according to the value of format_out. Chromatograms may be returned in either wide or long format according to the value of data_format.

Details

Provides a unified interface to all chromConverter parsers. Currently recognizes 'Agilent ChemStation' (.uv, .ch, .dx), 'Agilent MassHunter' (.dad), 'Thermo RAW' (.raw), 'Waters ARW' (.arw), 'Waters RAW' (.raw), 'Chromeleon ASCII' (.txt), 'Shimadzu ASCII' (.txt), 'Shimadzu GCD' (.gcd), 'Shimadzu LCD' (.lcd, DAD and chromatogram streams) and 'Shimadzu QGD' (.qgd) files. Also, wraps 'OpenChrom' parsers, which include many additional formats. To use 'Entab', 'ThermoRawFileParser', or 'OpenChrom' parsers, they must be separately installed. Please see the instructions in the README for further details.

If paths to individual files are provided, read_chroms will try to infer the file format and select an appropriate parser. However, when providing paths to directories, the file format must be specified using the format_in argument.

Side effects

If export_format is provided, chromatograms will be exported in the specified format specified into the folder specified by path_out. Files can currently be converted to csv, mzml, cdf, arw. If an openchrom parser is selected, ANIML format is available as an additional option.

Author

Ethan Bass

Examples

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