read_chroms {chromConverter}

Read Chromatograms

Description

Reads chromatograms from specified folders or vector of paths using file parsers from Aston, Entab, and ThermoRawFileParser.

Usage

read_chroms(
  paths,
  find_files,
  format_in = c("chemstation_uv", "chemstation_csv", "masshunter_dad", "shimadzu_fid",
    "shimadzu_dad", "chromeleon_uv", "thermoraw", "mzml", "waters_arw", "msd", "csd",
    "wsd", "other"),
  pattern = NULL,
  parser = c("", "chromconverter", "aston", "entab", "thermoraw", "openchrom"),
  format_out = c("matrix", "data.frame"),
  export = FALSE,
  path_out = NULL,
  export_format = c("csv", "cdf", "mzml", "animl"),
  read_metadata = TRUE,
  dat = NULL
)

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. The current options are: chemstation_uv, chemstation_csv, masshunter_dad, shimadzu_fid, shimadzu_dad, chromeleon_uv, thermoraw, mzml, waters_arw, msd, csd, wsd, or other.

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. Current option are chromconverter, aston, entab, thermoraw, or openchrom.

format_out

R object format (i.e. data.frame or matrix).

export

Logical. If TRUE, will export files as csvs.

path_out

Path for exporting files. If path not specified, files will export to current working directory.

export_format

Export format. Currently the only option is .csv, unless you are using OpenChrom parsers, where you could have csv, cdf, mzml, or animl.

read_metadata

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

dat

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

Details

Currently recognizes Agilent ChemStation '.uv', MassHunter '.dad' files, and ThermoRaw files. To use Entab and the ThermoRawFileParser, they must be manually installed. Please see the instructions in the Read Me.

Value

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

Side effects

If export is TRUE, chromatograms will be exported in the format specified by export_format in the folder specified by path_out. Currently, the only option for export is csv unless the parser is openchrom.

Author(s)

Ethan Bass

Examples

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